From 75e14e9c751e840310b85a7edc28a5efa3303911 Mon Sep 17 00:00:00 2001
From: Magali Ruffier <mr6@ebi.ac.uk>
Date: Fri, 6 May 2016 15:55:07 +0100
Subject: [PATCH] add latest patches

---
 .../circ/core/SQLite/table.sql                |  339 +-
 modules/t/test-genome-DBs/circ/core/gene.txt  |  518 +--
 modules/t/test-genome-DBs/circ/core/meta.txt  |    1 +
 modules/t/test-genome-DBs/circ/core/table.sql |  206 +-
 .../test-genome-DBs/circ/core/transcript.txt  |  518 +--
 .../homo_sapiens/core/SQLite/table.sql        |  332 +-
 .../homo_sapiens/core/exon.txt                |    2 +-
 .../homo_sapiens/core/gene.txt                |    2 +-
 .../homo_sapiens/core/meta.txt                |    1 +
 .../homo_sapiens/core/table.sql               |  260 +-
 .../homo_sapiens/empty/SQLite/table.sql       |   21 +-
 .../homo_sapiens/empty/meta.txt               |    1 +
 .../homo_sapiens/empty/table.sql              |  196 +-
 .../homo_sapiens/patch/SQLite/table.sql       |   14 +-
 .../homo_sapiens/patch/meta.txt               |    1 +
 .../homo_sapiens/patch/table.sql              |  258 +-
 .../homo_sapiens/variation/SQLite/table.sql   |  781 ++++
 .../homo_sapiens/variation/meta.txt           |    7 +-
 .../homo_sapiens/variation/table.sql          |   52 +-
 .../mapping/core/SQLite/table.sql             |  332 +-
 .../t/test-genome-DBs/mapping/core/meta.txt   |    3 +-
 .../t/test-genome-DBs/mapping/core/table.sql  |  188 +-
 .../mus_musculus/core/SQLite/table.sql        |  352 +-
 .../mus_musculus/core/meta.txt                |    1 +
 .../mus_musculus/core/table.sql               |  190 +-
 .../mus_musculus/variation/SQLite/table.sql   |   26 +-
 .../mus_musculus/variation/meta.txt           |    7 +-
 .../mus_musculus/variation/table.sql          |   26 +-
 .../nameless/core/SQLite/table.sql            |  332 +-
 .../t/test-genome-DBs/nameless/core/meta.txt  |    1 +
 .../t/test-genome-DBs/nameless/core/table.sql |  182 +-
 .../ontology/ontology/SQLite/table.sql        |    8 +-
 .../ontology/ontology/closure.txt             | 3528 ++++++++---------
 .../ontology/ontology/meta.txt                |    2 +
 .../ontology/ontology/table.sql               |    4 +-
 .../polyploidy/core/SQLite/table.sql          |  332 +-
 .../test-genome-DBs/polyploidy/core/meta.txt  |    1 +
 .../test-genome-DBs/polyploidy/core/table.sql |  212 +-
 .../test_collection/core/SQLite/table.sql     |  339 +-
 .../test_collection/core/meta.txt             |    1 +
 .../test_collection/core/table.sql            |  182 +-
 41 files changed, 5267 insertions(+), 4492 deletions(-)

diff --git a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
index 4211f0410d..62065f2443 100644
--- a/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:10 2015
+-- Created on Fri May  6 15:43:37 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL,
-  type varchar(30) NOT NULL,
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,11 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -303,14 +301,12 @@ CREATE TABLE external_db (
   description text
 );
 
-CREATE UNIQUE INDEX db_name_idx ON external_db (db_name, db_release);
-
 --
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -380,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -396,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -418,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -437,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -451,8 +447,7 @@ CREATE TABLE mapping_session (
   new_release varchar(5) NOT NULL DEFAULT '',
   old_assembly varchar(20) NOT NULL DEFAULT '',
   new_assembly varchar(20) NOT NULL DEFAULT '',
-  created datetime NOT NULL,
-  species_id integer NOT NULL
+  created datetime NOT NULL
 );
 
 --
@@ -472,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -485,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -497,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -511,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -523,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -532,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -578,35 +573,35 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
 --
 CREATE TABLE ontology_xref (
   object_xref_id integer NOT NULL DEFAULT 0,
-  source_xref_id integer,
-  linkage_type varchar(3)
+  linkage_type varchar(3),
+  source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -620,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -638,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -665,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -681,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -694,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -715,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision,
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -736,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -747,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -763,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -797,7 +792,7 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
 CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
@@ -807,12 +802,12 @@ CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -825,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -861,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -912,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -934,7 +929,7 @@ CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, a
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -945,8 +940,6 @@ CREATE TABLE unmapped_object (
   parent varchar(255)
 );
 
-CREATE UNIQUE INDEX unique_unmapped_obj_idx ON unmapped_object (ensembl_id, ensembl_object_type, identifier, unmapped_reason_id, parent, external_db_id);
-
 --
 -- Table: unmapped_reason
 --
diff --git a/modules/t/test-genome-DBs/circ/core/gene.txt b/modules/t/test-genome-DBs/circ/core/gene.txt
index e5353dd632..9c1226485f 100644
--- a/modules/t/test-genome-DBs/circ/core/gene.txt
+++ b/modules/t/test-genome-DBs/circ/core/gene.txt
@@ -1,259 +1,259 @@
-6626	protein_coding	21	3	700	2754	-1	88455	ensembl	ANNOTATED	hypothetical protein	1	6626	BTF1_30582	1	2013-07-16 13:03:32	2013-07-16 13:03:32
-6627	protein_coding	21	3	2758	4539	-1	88463	ensembl	ANNOTATED	hypothetical protein	1	6627	BTF1_30587	1	2013-07-16 13:03:51	2013-07-16 13:03:51
-6628	protein_coding	21	3	4552	5766	-1	88472	ensembl	ANNOTATED	hypothetical protein	1	6628	BTF1_30592	1	2013-07-16 13:03:57	2013-07-16 13:03:57
-6629	protein_coding	21	3	5781	6728	-1	88480	ensembl	ANNOTATED	hypothetical protein	1	6629	BTF1_30597	1	2013-07-16 13:03:17	2013-07-16 13:03:17
-6630	protein_coding	21	3	6744	7493	-1	88488	ensembl	ANNOTATED	hypothetical protein	1	6630	BTF1_30602	1	2013-07-16 13:03:24	2013-07-16 13:03:24
-6631	protein_coding	21	3	7496	7870	-1	88496	ensembl	ANNOTATED	hypothetical protein	1	6631	BTF1_30607	1	2013-07-16 13:03:25	2013-07-16 13:03:25
-6632	protein_coding	21	3	7968	8195	-1	88504	ensembl	ANNOTATED	hypothetical protein	1	6632	BTF1_30612	1	2013-07-16 13:04:10	2013-07-16 13:04:10
-6633	protein_coding	21	3	8271	8933	-1	88512	ensembl	ANNOTATED	hypothetical protein	1	6633	BTF1_30617	1	2013-07-16 13:04:09	2013-07-16 13:04:09
-6634	protein_coding	21	3	230089	230622	1	88521	ensembl	ANNOTATED	hypothetical protein	1	6634	BTF1_31742	1	2013-07-16 13:03:54	2013-07-16 13:03:54
-6635	protein_coding	21	3	230700	230885	1	88529	ensembl	ANNOTATED	hypothetical protein	1	6635	BTF1_31747	1	2013-07-16 13:03:16	2013-07-16 13:03:16
-6636	protein_coding	21	3	230948	231418	1	88537	ensembl	ANNOTATED	hypothetical protein	1	6636	BTF1_31752	1	2013-07-16 13:03:37	2013-07-16 13:03:37
-6637	protein_coding	21	3	231603	231902	1	88545	ensembl	ANNOTATED	hypothetical protein	1	6637	BTF1_31757	1	2013-07-16 13:04:15	2013-07-16 13:04:15
-6638	protein_coding	21	3	232697	232912	1	88553	ensembl	ANNOTATED	hypothetical protein	1	6638	BTF1_31762	1	2013-07-16 13:03:31	2013-07-16 13:03:31
-6639	protein_coding	21	3	232927	233595	-1	88561	ensembl	ANNOTATED	hypothetical protein	1	6639	BTF1_31767	1	2013-07-16 13:04:11	2013-07-16 13:04:11
-6640	protein_coding	21	3	233785	233991	1	88569	ensembl	ANNOTATED	hypothetical protein	1	6640	BTF1_31772	1	2013-07-16 13:03:49	2013-07-16 13:03:49
-6641	protein_coding	21	3	234076	235323	-1	88577	ensembl	ANNOTATED	hypothetical protein	1	6641	BTF1_31777	1	2013-07-16 13:03:34	2013-07-16 13:03:34
-6642	protein_coding	21	3	235337	685	-1	88585	ensembl	ANNOTATED	hypothetical protein	1	6642	BTF1_30577	1	2013-07-16 13:03:58	2013-07-16 13:03:58
-6643	protein_coding	21	3	150202	151044	1	88594	ensembl	ANNOTATED	ThiF family protein	1	6643	BTF1_31212	1	2013-07-16 13:03:44	2013-07-16 13:03:44
-6644	protein_coding	21	3	151325	153892	1	88609	ensembl	ANNOTATED	hypothetical protein	1	6644	BTF1_31217	1	2013-07-16 13:04:07	2013-07-16 13:04:07
-6645	protein_coding	21	3	153966	154949	1	88618	ensembl	ANNOTATED	N-acetylmuramoyl-L-alanine amidase	1	6645	BTF1_31222	1	2013-07-16 13:04:11	2013-07-16 13:04:11
-6646	tRNA	28	3	155169	155243	1	88632	ensembl	ANNOTATED	\N	1	6646	BTF1_t31789	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6647	tRNA	28	3	155250	155329	1	88635	ensembl	ANNOTATED	\N	1	6647	BTF1_t31791	1	2013-07-16 13:04:16	2013-07-16 13:04:16
-6648	tRNA	28	3	155338	155425	1	88638	ensembl	ANNOTATED	\N	1	6648	BTF1_t31793	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6649	tRNA	28	3	155623	155697	1	88641	ensembl	ANNOTATED	\N	1	6649	BTF1_t31795	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6650	tRNA	28	3	155704	155775	1	88644	ensembl	ANNOTATED	\N	1	6650	BTF1_t31797	1	2013-07-16 13:04:18	2013-07-16 13:04:18
-6651	tRNA	28	3	155782	155854	1	88647	ensembl	ANNOTATED	\N	1	6651	BTF1_t31799	1	2013-07-16 13:04:18	2013-07-16 13:04:18
-6652	tRNA	28	3	156057	156133	1	88650	ensembl	ANNOTATED	\N	1	6652	BTF1_t31801	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6653	tRNA	28	3	156290	156363	1	88653	ensembl	ANNOTATED	\N	1	6653	BTF1_t31803	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6654	tRNA	28	3	156374	156448	1	88656	ensembl	ANNOTATED	\N	1	6654	BTF1_t31805	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6655	tRNA	28	3	156548	156621	1	88659	ensembl	ANNOTATED	\N	1	6655	BTF1_t31807	1	2013-07-16 13:04:16	2013-07-16 13:04:16
-6656	tRNA	28	3	156632	156705	1	88662	ensembl	ANNOTATED	\N	1	6656	BTF1_t31809	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6657	tRNA	28	3	156735	156807	1	88665	ensembl	ANNOTATED	\N	1	6657	BTF1_t31811	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6658	protein_coding	21	3	156856	157386	1	88668	ensembl	ANNOTATED	hypothetical protein	1	6658	BTF1_31227	1	2013-07-16 13:03:59	2013-07-16 13:03:59
-6659	tRNA	28	3	157418	157494	1	88676	ensembl	ANNOTATED	\N	1	6659	BTF1_t31813	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6660	tRNA	28	3	157503	157575	1	88679	ensembl	ANNOTATED	\N	1	6660	BTF1_t31815	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6661	tRNA	28	3	157852	157935	1	88682	ensembl	ANNOTATED	\N	1	6661	BTF1_t31817	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6662	tRNA	28	3	157939	158012	1	88685	ensembl	ANNOTATED	\N	1	6662	BTF1_t31819	1	2013-07-16 13:04:18	2013-07-16 13:04:18
-6663	tRNA	28	3	158104	158192	1	88688	ensembl	ANNOTATED	\N	1	6663	BTF1_t31821	1	2013-07-16 13:04:16	2013-07-16 13:04:16
-6664	protein_coding	21	3	158412	158852	1	88691	ensembl	ANNOTATED	hypothetical protein	1	6664	BTF1_31237	1	2013-07-16 13:04:12	2013-07-16 13:04:12
-6665	protein_coding	21	3	158878	159462	1	88700	ensembl	ANNOTATED	thymidine kinase	1	6665	BTF1_31242	1	2013-07-16 13:03:39	2013-07-16 13:03:39
-6666	protein_coding	21	3	159476	159976	1	88717	ensembl	ANNOTATED	hypothetical protein	1	6666	BTF1_31247	1	2013-07-16 13:03:17	2013-07-16 13:03:17
-6667	protein_coding	21	3	159997	160533	1	88726	ensembl	ANNOTATED	single-strand binding protein family	1	6667	BTF1_31252	1	2013-07-16 13:03:43	2013-07-16 13:03:43
-6668	protein_coding	21	4	210132	210989	1	88741	ensembl	ANNOTATED	hypothetical protein	1	6668	BTF1_32826	1	2013-07-16 13:04:34	2013-07-16 13:04:34
-6669	protein_coding	21	4	211116	212180	1	88749	ensembl	ANNOTATED	hypothetical protein	1	6669	BTF1_32831	1	2013-07-16 13:04:43	2013-07-16 13:04:43
-6670	protein_coding	21	4	212807	213178	1	88757	ensembl	ANNOTATED	hypothetical protein	1	6670	BTF1_32841	1	2013-07-16 13:04:52	2013-07-16 13:04:52
-6671	protein_coding	21	4	213615	213926	1	88765	ensembl	ANNOTATED	hypothetical protein	1	6671	BTF1_32846	1	2013-07-16 13:04:34	2013-07-16 13:04:34
-6672	protein_coding	21	4	213957	214370	1	88775	ensembl	ANNOTATED	hypothetical protein	1	6672	BTF1_32851	1	2013-07-16 13:05:04	2013-07-16 13:05:04
-6673	protein_coding	21	4	215358	215726	1	88788	ensembl	ANNOTATED	hypothetical protein	1	6673	BTF1_32856	1	2013-07-16 13:04:44	2013-07-16 13:04:44
-6674	protein_coding	21	4	215708	216049	1	88797	ensembl	ANNOTATED	hypothetical protein	1	6674	BTF1_32861	1	2013-07-16 13:04:33	2013-07-16 13:04:33
-6675	protein_coding	21	4	216280	217335	1	88805	ensembl	ANNOTATED	hypothetical protein	1	6675	BTF1_32866	1	2013-07-16 13:05:02	2013-07-16 13:05:02
-6676	protein_coding	21	4	217755	218327	1	88814	ensembl	ANNOTATED	hypothetical protein	1	6676	BTF1_32871	1	2013-07-16 13:05:03	2013-07-16 13:05:03
-6677	protein_coding	21	4	218689	219771	1	88823	ensembl	ANNOTATED	1-phosphatidylinositol phosphodiesterase	1	6677	BTF1_32876	1	2013-07-16 13:05:05	2013-07-16 13:05:05
-6678	protein_coding	21	4	220171	220830	-1	88838	ensembl	ANNOTATED	Hypothetical protein	1	6678	BTF1_32881	1	2013-07-16 13:04:36	2013-07-16 13:04:36
-6679	protein_coding	21	4	221204	221416	1	88852	ensembl	ANNOTATED	methionine-rich protein	1	6679	BTF1_32886	1	2013-07-16 13:04:24	2013-07-16 13:04:24
-6680	protein_coding	21	4	221988	222215	1	88861	ensembl	ANNOTATED	integrase protein	1	6680	BTF1_32891	1	2013-07-16 13:04:46	2013-07-16 13:04:46
-6681	protein_coding	21	4	222287	432	1	88879	ensembl	ANNOTATED	transposase Tn3	1	6681	BTF1_32896	1	2013-07-16 13:04:21	2013-07-16 13:04:21
-6682	protein_coding	21	4	572	1483	-1	88893	ensembl	ANNOTATED	crystal protein	1	6682	BTF1_31826	1	2013-07-16 13:04:22	2013-07-16 13:04:22
-6683	protein_coding	21	4	1640	2599	-1	88903	ensembl	ANNOTATED	crystal protein	1	6683	BTF1_31831	1	2013-07-16 13:04:31	2013-07-16 13:04:31
-6684	protein_coding	21	4	2873	3121	1	88914	ensembl	ANNOTATED	hypothetical protein	1	6684	BTF1_31836	1	2013-07-16 13:04:43	2013-07-16 13:04:43
-6685	protein_coding	21	4	3135	3731	1	88923	ensembl	ANNOTATED	insertion sequence IS240 protein	1	6685	BTF1_31841	1	2013-07-16 13:04:43	2013-07-16 13:04:43
-6686	protein_coding	21	4	3847	4158	-1	88937	ensembl	ANNOTATED	hypothetical protein	1	6686	BTF1_31846	1	2013-07-16 13:05:02	2013-07-16 13:05:02
-6687	protein_coding	21	4	4626	5060	-1	88946	ensembl	ANNOTATED	hypothetical protein	1	6687	BTF1_31851	1	2013-07-16 13:04:38	2013-07-16 13:04:38
-6688	protein_coding	21	4	5444	6019	-1	88954	ensembl	ANNOTATED	hypothetical protein	1	6688	BTF1_31856	1	2013-07-16 13:04:53	2013-07-16 13:04:53
-6689	protein_coding	21	4	7087	8286	-1	88963	ensembl	ANNOTATED	major facilitator superfamily protein	1	6689	BTF1_31871	1	2013-07-16 13:04:41	2013-07-16 13:04:41
-6690	protein_coding	21	4	8316	8516	-1	88978	ensembl	ANNOTATED	IS4 family transposase	1	6690	BTF1_31876	1	2013-07-16 13:05:05	2013-07-16 13:05:05
-6691	protein_coding	21	4	8683	8943	-1	88986	ensembl	ANNOTATED	hypothetical protein	1	6691	BTF1_31881	1	2013-07-16 13:05:01	2013-07-16 13:05:01
-6692	protein_coding	21	4	9011	10948	-1	88994	ensembl	ANNOTATED	hypothetical protein	1	6692	BTF1_31886	1	2013-07-16 13:04:45	2013-07-16 13:04:45
-6693	protein_coding	21	7	347058	347492	-1	89002	ensembl	ANNOTATED	hypothetical protein	1	6693	BTF1_30562	1	2013-07-16 13:05:41	2013-07-16 13:05:41
-6694	protein_coding	21	7	347641	348741	-1	89010	ensembl	ANNOTATED	hypothetical protein	1	6694	BTF1_30567	1	2013-07-16 13:06:06	2013-07-16 13:06:06
-6695	protein_coding	21	7	348754	349407	-1	89018	ensembl	ANNOTATED	hypothetical protein	1	6695	BTF1_30572	1	2013-07-16 13:06:29	2013-07-16 13:06:29
-6696	protein_coding	21	7	349459	333	-1	89026	ensembl	ANNOTATED	hypothetical protein	1	6696	BTF1_28407	1	2013-07-16 13:06:14	2013-07-16 13:06:14
-6697	protein_coding	21	7	453	1598	-1	89034	ensembl	ANNOTATED	hypothetical protein	1	6697	BTF1_28412	1	2013-07-16 13:06:04	2013-07-16 13:06:04
-6698	protein_coding	21	7	1612	1947	-1	89042	ensembl	ANNOTATED	hypothetical protein	1	6698	BTF1_28417	1	2013-07-16 13:05:49	2013-07-16 13:05:49
-6699	protein_coding	21	7	2425	2937	-1	89050	ensembl	ANNOTATED	hypothetical protein	1	6699	BTF1_28422	1	2013-07-16 13:05:26	2013-07-16 13:05:26
-6700	protein_coding	21	7	2957	3427	-1	89058	ensembl	ANNOTATED	hypothetical protein	1	6700	BTF1_28427	1	2013-07-16 13:05:35	2013-07-16 13:05:35
-6701	protein_coding	21	7	3458	3892	-1	89066	ensembl	ANNOTATED	hypothetical protein	1	6701	BTF1_28432	1	2013-07-16 13:05:15	2013-07-16 13:05:15
-6702	protein_coding	21	7	4042	4494	-1	89074	ensembl	ANNOTATED	hypothetical protein	1	6702	BTF1_28437	1	2013-07-16 13:05:33	2013-07-16 13:05:33
-6703	protein_coding	21	7	4528	4965	-1	89082	ensembl	ANNOTATED	hypothetical protein	1	6703	BTF1_28442	1	2013-07-16 13:05:38	2013-07-16 13:05:38
-6704	protein_coding	21	11	5300113	5300397	1	89090	ensembl	ANNOTATED	hypothetical protein	1	6704	BTF1_27315	1	2013-07-16 13:09:18	2013-07-16 13:09:18
-6705	protein_coding	21	11	5300922	5301548	1	89098	ensembl	ANNOTATED	hypothetical protein	1	6705	BTF1_27320	1	2013-07-16 13:31:48	2013-07-16 13:31:48
-6706	protein_coding	21	11	5301578	5302180	1	89107	ensembl	ANNOTATED	putative prophage LambdaBa01, prohead protease	1	6706	BTF1_27325	1	2013-07-16 13:25:20	2013-07-16 13:25:20
-6707	protein_coding	21	11	5302408	5303115	1	89120	ensembl	ANNOTATED	hypothetical protein	1	6707	BTF1_27330	1	2013-07-16 13:12:50	2013-07-16 13:12:50
-6708	protein_coding	21	11	5303151	5304335	1	89129	ensembl	ANNOTATED	putative DNA-binding protein	1	6708	BTF1_27335	1	2013-07-16 13:15:34	2013-07-16 13:15:34
-6709	protein_coding	21	11	5304508	5305038	-1	89142	ensembl	ANNOTATED	hypothetical protein	1	6709	BTF1_27340	1	2013-07-16 13:36:54	2013-07-16 13:36:54
-6710	protein_coding	21	11	5305053	5306660	-1	89151	ensembl	ANNOTATED	hypothetical protein	1	6710	BTF1_27345	1	2013-07-16 13:29:49	2013-07-16 13:29:49
-6711	protein_coding	21	11	5306860	5307246	1	89165	ensembl	ANNOTATED	putative prophage LambdaBa04, DNA binding protein	1	6711	BTF1_27350	1	2013-07-16 13:24:02	2013-07-16 13:24:02
-6712	protein_coding	21	11	5308066	5309604	1	89175	ensembl	ANNOTATED	GMP synthase	1	6712	BTF1_27355	1	2013-07-16 13:09:04	2013-07-16 13:09:04
-6713	protein_coding	21	11	5309909	5310424	1	89204	ensembl	ANNOTATED	hypothetical protein	1	6713	BTF1_27360	1	2013-07-16 13:30:56	2013-07-16 13:30:56
-6714	protein_coding	21	11	5310421	5311137	1	89212	ensembl	ANNOTATED	hypothetical protein	1	6714	BTF1_27365	1	2013-07-16 13:26:15	2013-07-16 13:26:15
-6715	protein_coding	21	11	5311140	5312159	1	89220	ensembl	ANNOTATED	hypothetical protein	1	6715	BTF1_27370	1	2013-07-16 13:07:13	2013-07-16 13:07:13
-6716	protein_coding	21	11	5312477	5312884	1	89228	ensembl	ANNOTATED	hypothetical protein	1	6716	BTF1_27375	1	2013-07-16 13:40:17	2013-07-16 13:40:17
-6717	protein_coding	21	11	5313273	5313545	1	89236	ensembl	ANNOTATED	hypothetical protein	1	6717	BTF1_27380	1	2013-07-16 13:37:40	2013-07-16 13:37:40
-6718	protein_coding	21	11	5313814	5315220	1	89245	ensembl	ANNOTATED	FtsK/SpoIIIE family protein	1	6718	BTF1_27385	1	2013-07-16 13:39:16	2013-07-16 13:39:16
-6719	protein_coding	21	11	5315514	5316017	1	89267	ensembl	ANNOTATED	hypothetical protein	1	6719	BTF1_27390	1	2013-07-16 13:14:28	2013-07-16 13:14:28
-6720	protein_coding	21	11	5315998	5317026	1	89276	ensembl	ANNOTATED	replication initiation factor	1	6720	BTF1_27395	1	2013-07-16 13:08:35	2013-07-16 13:08:35
-6721	protein_coding	21	11	5317047	5317253	1	89291	ensembl	ANNOTATED	hypothetical protein	1	6721	BTF1_27400	1	2013-07-16 13:38:43	2013-07-16 13:38:43
-6722	protein_coding	21	11	5317250	5318503	1	89301	ensembl	ANNOTATED	integrase family protein	1	6722	BTF1_27405	1	2013-07-16 13:29:35	2013-07-16 13:29:35
-6723	protein_coding	21	11	5318504	5319310	1	89320	ensembl	ANNOTATED	serine/threonine protein phosphatase	1	6723	BTF1_27410	1	2013-07-16 13:09:02	2013-07-16 13:09:02
-6724	protein_coding	21	11	5319297	5319689	1	89332	ensembl	ANNOTATED	hypothetical protein	1	6724	BTF1_27415	1	2013-07-16 13:42:07	2013-07-16 13:42:07
-6725	protein_coding	21	11	5320179	5321504	1	89341	ensembl	ANNOTATED	xanthine/uracil permease	1	6725	BTF1_27420	1	2013-07-16 13:12:33	2013-07-16 13:12:33
-6726	protein_coding	21	11	5321798	5322499	1	89358	ensembl	ANNOTATED	two-component response regulator	1	6726	BTF1_27425	1	2013-07-16 13:43:11	2013-07-16 13:43:11
-6727	protein_coding	21	11	5322483	5323988	1	89379	ensembl	ANNOTATED	two component system histidine kinase	1	6727	BTF1_27430	1	2013-07-16 13:23:41	2013-07-16 13:23:41
-6728	rRNA	28	11	5324281	5325843	1	89401	ensembl	ANNOTATED	\N	1	6728	BTF1_r28371	1	2013-07-16 13:44:01	2013-07-16 13:44:01
-6729	rRNA	28	11	5325982	5328906	1	89404	ensembl	ANNOTATED	\N	1	6729	BTF1_r28399	1	2013-07-16 13:43:58	2013-07-16 13:43:58
-6730	rRNA	28	11	5328953	5329068	1	89407	ensembl	ANNOTATED	\N	1	6730	BTF1_r28343	1	2013-07-16 13:44:00	2013-07-16 13:44:00
-6731	protein_coding	21	11	5329301	5330260	1	89411	ensembl	ANNOTATED	alpha/beta hydrolase	1	6731	BTF1_27435	1	2013-07-16 13:36:53	2013-07-16 13:36:53
-6732	protein_coding	21	11	5330461	5331192	1	89423	ensembl	ANNOTATED	FrnE protein	1	6732	BTF1_27440	1	2013-07-16 13:38:09	2013-07-16 13:38:09
-6733	rRNA	28	11	5331540	5333102	1	89435	ensembl	ANNOTATED	\N	1	6733	BTF1_r28373	1	2013-07-16 13:43:54	2013-07-16 13:43:54
-6734	rRNA	28	11	5333241	5336165	1	89438	ensembl	ANNOTATED	\N	1	6734	BTF1_r28401	1	2013-07-16 13:43:54	2013-07-16 13:43:54
-6735	rRNA	28	11	5336211	5336326	1	89441	ensembl	ANNOTATED	\N	1	6735	BTF1_r28345	1	2013-07-16 13:43:59	2013-07-16 13:43:59
-6736	protein_coding	21	11	5336495	5336923	-1	89445	ensembl	ANNOTATED	GntR family transcriptional regulator	1	6736	BTF1_27445	1	2013-07-16 13:15:40	2013-07-16 13:15:40
-6737	rRNA	28	11	5339054	5340616	1	89461	ensembl	ANNOTATED	\N	1	6737	BTF1_r28375	1	2013-07-16 13:43:55	2013-07-16 13:43:55
-6738	rRNA	28	11	5340755	5343679	1	89464	ensembl	ANNOTATED	\N	1	6738	BTF1_r28403	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6739	rRNA	28	11	5343725	5343840	1	89467	ensembl	ANNOTATED	\N	1	6739	BTF1_r28347	1	2013-07-16 13:43:57	2013-07-16 13:43:57
-6740	protein_coding	21	11	5343916	5344374	-1	89470	ensembl	ANNOTATED	asch domain superfamily protein	1	6740	BTF1_27460	1	2013-07-16 13:15:03	2013-07-16 13:15:03
-6741	protein_coding	21	11	5344731	5345528	-1	89482	ensembl	ANNOTATED	undecaprenyl pyrophosphate phosphatase	1	6741	BTF1_27465	1	2013-07-16 13:29:26	2013-07-16 13:29:26
-6742	protein_coding	21	11	5345546	5346283	-1	89505	ensembl	ANNOTATED	bacitracin ABC transporter permease	1	6742	BTF1_27470	1	2013-07-16 13:34:14	2013-07-16 13:34:14
-6743	protein_coding	21	11	5346276	5347205	-1	89514	ensembl	ANNOTATED	bacitracin ABC transporter ATP-binding protein	1	6743	BTF1_27475	1	2013-07-16 13:27:09	2013-07-16 13:27:09
-6744	protein_coding	21	11	5347274	5348287	-1	89533	ensembl	ANNOTATED	sensor histidine kinase	1	6744	BTF1_27480	1	2013-07-16 13:20:05	2013-07-16 13:20:05
-6745	protein_coding	21	11	5348277	5348990	-1	89557	ensembl	ANNOTATED	DNA-binding response regulator	1	6745	BTF1_27485	1	2013-07-16 13:33:30	2013-07-16 13:33:30
-6746	rRNA	28	11	5349468	5351030	1	89577	ensembl	ANNOTATED	\N	1	6746	BTF1_r28377	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6747	rRNA	28	11	5351169	5354093	1	89580	ensembl	ANNOTATED	\N	1	6747	BTF1_r28405	1	2013-07-16 13:43:54	2013-07-16 13:43:54
-6748	rRNA	28	11	5354139	5354254	1	89583	ensembl	ANNOTATED	\N	1	6748	BTF1_r28349	1	2013-07-16 13:43:58	2013-07-16 13:43:58
-6749	protein_coding	21	11	5354467	5355387	1	89587	ensembl	ANNOTATED	transporter Drug/Metabolite Exporter family protein	1	6749	BTF1_27490	1	2013-07-16 13:23:57	2013-07-16 13:23:57
-6750	protein_coding	21	11	5355474	5356265	-1	89599	ensembl	ANNOTATED	hypothetical protein	1	6750	BTF1_27495	1	2013-07-16 13:21:59	2013-07-16 13:21:59
-6751	rRNA	28	11	5356579	5358141	1	89612	ensembl	ANNOTATED	\N	1	6751	BTF1_r28379	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6752	rRNA	28	11	5358280	5361204	1	89615	ensembl	ANNOTATED	\N	1	6752	BTF1_r28407	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6753	rRNA	28	11	5361251	5361366	1	89618	ensembl	ANNOTATED	\N	1	6753	BTF1_r28351	1	2013-07-16 13:43:55	2013-07-16 13:43:55
-6754	protein_coding	21	11	5362106	5362591	1	89622	ensembl	ANNOTATED	phosphoribosylaminoimidazole carboxylase catalytic subunit	1	6754	BTF1_27500	1	2013-07-16 13:12:36	2013-07-16 13:12:36
-6755	protein_coding	21	11	5362588	5363739	1	89637	ensembl	ANNOTATED	phosphoribosylaminoimidazole carboxylase ATPase subunit	1	6755	BTF1_27505	1	2013-07-16 13:07:35	2013-07-16 13:07:35
-6756	protein_coding	21	11	5363736	5365043	1	89666	ensembl	ANNOTATED	adenylosuccinate lyase	1	6756	BTF1_27510	1	2013-07-16 13:17:58	2013-07-16 13:17:58
-6757	protein_coding	21	11	5365132	5365851	1	89689	ensembl	ANNOTATED	phosphoribosylaminoimidazole-succinocarboxamide synthase	1	6757	BTF1_27515	1	2013-07-16 13:14:58	2013-07-16 13:14:58
-6758	protein_coding	21	11	5365844	5366098	1	89707	ensembl	ANNOTATED	phosphoribosylformylglycinamidine synthase subunit PurS	1	6758	BTF1_27520	1	2013-07-16 13:12:48	2013-07-16 13:12:48
-6759	protein_coding	21	11	5366095	5366778	1	89719	ensembl	ANNOTATED	phosphoribosylformylglycinamidine synthase I	1	6759	BTF1_27525	1	2013-07-16 13:20:46	2013-07-16 13:20:46
-6760	protein_coding	21	11	5366762	5368981	1	89740	ensembl	ANNOTATED	phosphoribosylformylglycinamidine synthase II	1	6760	BTF1_27530	1	2013-07-16 13:29:17	2013-07-16 13:29:17
-6761	protein_coding	21	11	5368966	5370381	1	89761	ensembl	ANNOTATED	amidophosphoribosyltransferase	1	6761	BTF1_27535	1	2013-07-16 13:10:58	2013-07-16 13:10:58
-6762	protein_coding	21	11	5370487	5371527	1	89784	ensembl	ANNOTATED	phosphoribosylaminoimidazole synthetase	1	6762	BTF1_27540	1	2013-07-16 13:36:20	2013-07-16 13:36:20
-6763	protein_coding	21	11	5371524	5372111	1	89805	ensembl	ANNOTATED	phosphoribosylglycinamide formyltransferase	1	6763	BTF1_27545	1	2013-07-16 13:23:37	2013-07-16 13:23:37
-6764	protein_coding	21	11	5372136	5373671	1	89825	ensembl	ANNOTATED	bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	1	6764	BTF1_27550	1	2013-07-16 13:40:41	2013-07-16 13:40:41
-6765	protein_coding	21	11	5374051	5375322	1	89844	ensembl	ANNOTATED	phosphoribosylamine--glycine ligase	1	6765	BTF1_27555	1	2013-07-16 13:22:35	2013-07-16 13:22:35
-6766	protein_coding	21	11	5375359	5375523	-1	89875	ensembl	ANNOTATED	hypothetical protein	1	6766	BTF1_27560	1	2013-07-16 13:41:32	2013-07-16 13:41:32
-6767	protein_coding	21	11	5375539	5376384	-1	89889	ensembl	ANNOTATED	hypothetical protein	1	6767	BTF1_27565	1	2013-07-16 13:27:17	2013-07-16 13:27:17
-6768	protein_coding	21	11	5376603	5376980	-1	89901	ensembl	ANNOTATED	hypothetical protein	1	6768	BTF1_27570	1	2013-07-16 13:42:21	2013-07-16 13:42:21
-6769	protein_coding	21	11	5377262	5377951	1	89911	ensembl	ANNOTATED	geranylgeranylglyceryl phosphate synthase-like protein	1	6769	BTF1_27575	1	2013-07-16 13:41:32	2013-07-16 13:41:32
-6770	protein_coding	21	11	5377952	5380213	1	89927	ensembl	ANNOTATED	ATP-dependent DNA helicase PcrA	1	6770	BTF1_27580	1	2013-07-16 13:30:44	2013-07-16 13:30:44
-6771	protein_coding	21	11	5380228	5382237	1	89952	ensembl	ANNOTATED	NAD-dependent DNA ligase LigA	1	6771	BTF1_27585	1	2013-07-16 13:16:58	2013-07-16 13:16:58
-6772	protein_coding	21	11	5382254	5383447	1	89980	ensembl	ANNOTATED	lipoprotein	1	6772	BTF1_27590	1	2013-07-16 13:26:19	2013-07-16 13:26:19
-6773	protein_coding	21	11	5383544	5384314	1	89990	ensembl	ANNOTATED	hypothetical protein	1	6773	BTF1_27595	1	2013-07-16 13:34:50	2013-07-16 13:34:50
-6774	protein_coding	21	11	5384468	5386015	1	90002	ensembl	ANNOTATED	1-pyrroline-5-carboxylate dehydrogenase	1	6774	BTF1_27600	1	2013-07-16 13:22:13	2013-07-16 13:22:13
-6775	protein_coding	21	11	5386286	5386831	-1	90027	ensembl	ANNOTATED	isochorismatase	1	6775	BTF1_27605	1	2013-07-16 13:38:42	2013-07-16 13:38:42
-6776	protein_coding	21	11	5387304	5388323	1	90039	ensembl	ANNOTATED	ABC transporter ATP-binding protein	1	6776	BTF1_27610	1	2013-07-16 13:25:57	2013-07-16 13:25:57
-6777	protein_coding	21	11	5388313	5388978	1	90065	ensembl	ANNOTATED	ABC transporter permease	1	6777	BTF1_27615	1	2013-07-16 13:08:07	2013-07-16 13:08:07
-6778	protein_coding	21	11	5389000	5389854	1	90080	ensembl	ANNOTATED	ABC transporter substrate-binding protein	1	6778	BTF1_27620	1	2013-07-16 13:22:04	2013-07-16 13:22:04
-6779	protein_coding	21	11	5390022	5390492	-1	90089	ensembl	ANNOTATED	hypothetical protein	1	6779	BTF1_27625	1	2013-07-16 13:25:05	2013-07-16 13:25:05
-6780	protein_coding	21	11	5390551	5390742	-1	90098	ensembl	ANNOTATED	hypothetical protein	1	6780	BTF1_27630	1	2013-07-16 13:06:45	2013-07-16 13:06:45
-6781	protein_coding	21	11	5390735	5391913	-1	90108	ensembl	ANNOTATED	anion-transporting ATPase	1	6781	BTF1_27635	1	2013-07-16 13:27:19	2013-07-16 13:27:19
-6782	protein_coding	21	11	5391992	5392474	-1	90126	ensembl	ANNOTATED	transcriptional regulator, MarR family protein	1	6782	BTF1_27640	1	2013-07-16 13:07:33	2013-07-16 13:07:33
-6783	protein_coding	21	11	5392706	5392942	1	90144	ensembl	ANNOTATED	hypothetical protein	1	6783	BTF1_27645	1	2013-07-16 13:23:54	2013-07-16 13:23:54
-6784	protein_coding	21	11	5393084	5393374	1	90154	ensembl	ANNOTATED	asparaginyl/glutamyl-tRNA amidotransferase subunit C	1	6784	BTF1_27650	1	2013-07-16 13:30:18	2013-07-16 13:30:18
-6785	protein_coding	21	11	5393390	5394847	1	90174	ensembl	ANNOTATED	aspartyl/glutamyl-tRNA amidotransferase subunit A	1	6785	BTF1_27655	1	2013-07-16 13:37:11	2013-07-16 13:37:11
-6786	protein_coding	21	11	5394862	5396289	1	90195	ensembl	ANNOTATED	aspartyl/glutamyl-tRNA amidotransferase subunit B	1	6786	BTF1_27660	1	2013-07-16 13:41:02	2013-07-16 13:41:02
-6787	protein_coding	21	11	5396850	5397755	1	90218	ensembl	ANNOTATED	lipid kinase	1	6787	BTF1_27665	1	2013-07-16 13:28:06	2013-07-16 13:28:06
-6788	protein_coding	21	11	5397896	5398642	1	90236	ensembl	ANNOTATED	haloacid dehalogenase/epoxide hydrolase	1	6788	BTF1_27670	1	2013-07-16 13:22:11	2013-07-16 13:22:11
-6789	protein_coding	21	11	5398797	5400161	1	90249	ensembl	ANNOTATED	4-aminobutyrate aminotransferase	1	6789	BTF1_27675	1	2013-07-16 13:20:01	2013-07-16 13:20:01
-6790	protein_coding	21	11	5400277	5401644	1	90269	ensembl	ANNOTATED	sigma-54-dependent transcriptional activator	1	6790	BTF1_27680	1	2013-07-16 13:22:46	2013-07-16 13:22:46
-6791	protein_coding	21	11	5401637	5403088	1	90301	ensembl	ANNOTATED	succinate-semialdehyde dehydrogenase	1	6791	BTF1_27685	1	2013-07-16 13:14:19	2013-07-16 13:14:19
-6792	protein_coding	21	11	5403136	5403459	1	90320	ensembl	ANNOTATED	quaternary ammonium	1	6792	BTF1_27690	1	2013-07-16 13:39:21	2013-07-16 13:39:21
-6793	protein_coding	21	11	5403592	5404083	1	90336	ensembl	ANNOTATED	hypothetical protein	1	6793	BTF1_27695	1	2013-07-16 13:09:08	2013-07-16 13:09:08
-6794	protein_coding	21	11	5404128	5405357	-1	90348	ensembl	ANNOTATED	aminopeptidase	1	6794	BTF1_27700	1	2013-07-16 13:26:05	2013-07-16 13:26:05
-6795	protein_coding	21	11	5405474	5406556	-1	90362	ensembl	ANNOTATED	polysaccharide deacetylase-like protein	1	6795	BTF1_27705	1	2013-07-16 13:41:01	2013-07-16 13:41:01
-6796	protein_coding	21	11	5406704	5406877	-1	90377	ensembl	ANNOTATED	hypothetical protein	1	6796	BTF1_27710	1	2013-07-16 13:35:08	2013-07-16 13:35:08
-6797	protein_coding	21	11	5407094	5407801	1	90385	ensembl	ANNOTATED	hypothetical protein	1	6797	BTF1_27715	1	2013-07-16 13:20:00	2013-07-16 13:20:00
-6798	protein_coding	21	11	5407848	5409044	-1	90394	ensembl	ANNOTATED	nucleoside permease nupC	1	6798	BTF1_27720	1	2013-07-16 13:41:35	2013-07-16 13:41:35
-6799	protein_coding	21	11	5409470	5410846	1	90413	ensembl	ANNOTATED	tRNA (Uracil-5-)-methyltransferase	1	6799	BTF1_27725	1	2013-07-16 13:36:03	2013-07-16 13:36:03
-6800	protein_coding	21	11	5411007	5411996	1	90435	ensembl	ANNOTATED	tRNA-dihydrouridine synthase	1	6800	BTF1_27730	1	2013-07-16 13:34:39	2013-07-16 13:34:39
-6801	protein_coding	21	11	5412348	5412866	1	90453	ensembl	ANNOTATED	hypothetical protein	1	6801	BTF1_27735	1	2013-07-16 13:08:22	2013-07-16 13:08:22
-6802	protein_coding	21	11	5412961	5413668	1	90463	ensembl	ANNOTATED	zinc metalloprotease	1	6802	BTF1_27740	1	2013-07-16 13:35:51	2013-07-16 13:35:51
-6803	protein_coding	21	11	5413665	5413856	-1	90476	ensembl	ANNOTATED	hypothetical protein	1	6803	BTF1_27745	1	2013-07-16 13:22:27	2013-07-16 13:22:27
-6804	protein_coding	21	11	5413888	5414583	-1	90485	ensembl	ANNOTATED	hypothetical protein	1	6804	BTF1_27750	1	2013-07-16 13:24:02	2013-07-16 13:24:02
-6805	protein_coding	21	11	5414598	5415707	-1	90498	ensembl	ANNOTATED	mandelate racemase/muconate lactonizing protein	1	6805	BTF1_27755	1	2013-07-16 13:25:27	2013-07-16 13:25:27
-6806	protein_coding	21	11	5415801	5417072	1	90511	ensembl	ANNOTATED	transcriptional regulator domain-containing protein	1	6806	BTF1_27760	1	2013-07-16 13:35:40	2013-07-16 13:35:40
-6807	protein_coding	21	11	5417061	5418482	-1	90520	ensembl	ANNOTATED	Na+/H+ antiporter NhaC	1	6807	BTF1_27765	1	2013-07-16 13:42:40	2013-07-16 13:42:40
-6808	protein_coding	21	11	5418775	5419890	1	90535	ensembl	ANNOTATED	amidohydrolase	1	6808	BTF1_27770	1	2013-07-16 13:36:58	2013-07-16 13:36:58
-6809	protein_coding	21	11	5420084	5420689	1	90548	ensembl	ANNOTATED	hypothetical protein	1	6809	BTF1_27775	1	2013-07-16 13:38:34	2013-07-16 13:38:34
-6810	protein_coding	21	11	5420722	5422248	-1	90557	ensembl	ANNOTATED	alkyl hydroperoxide reductase subunit F	1	6810	BTF1_27780	1	2013-07-16 13:19:13	2013-07-16 13:19:13
-6811	protein_coding	21	11	5422263	5422826	-1	90588	ensembl	ANNOTATED	Alkyl hydroperoxide reductase C22	1	6811	BTF1_27785	1	2013-07-16 13:18:31	2013-07-16 13:18:31
-6812	protein_coding	21	11	5423418	5424647	1	90608	ensembl	ANNOTATED	5-methylribose kinase	1	6812	BTF1_27790	1	2013-07-16 13:25:47	2013-07-16 13:25:47
-6813	protein_coding	21	11	5424657	5425703	1	90628	ensembl	ANNOTATED	methylthioribose-1-phosphate isomerase	1	6813	BTF1_27795	1	2013-07-16 13:21:46	2013-07-16 13:21:46
-6814	protein_coding	21	11	5425757	5426398	1	90647	ensembl	ANNOTATED	L-fuculose phosphate aldolase	1	6814	BTF1_27800	1	2013-07-16 13:37:42	2013-07-16 13:37:42
-6815	protein_coding	21	11	5426463	5427347	-1	90661	ensembl	ANNOTATED	integrase core domain-containing protein	1	6815	BTF1_27805	1	2013-07-16 13:18:06	2013-07-16 13:18:06
-6816	protein_coding	21	11	5427314	5427619	-1	90677	ensembl	ANNOTATED	transposase	1	6816	BTF1_27810	1	2013-07-16 13:17:04	2013-07-16 13:17:04
-6817	protein_coding	21	11	5427729	5428736	-1	90694	ensembl	ANNOTATED	iron compound ABC transporter permease	1	6817	BTF1_27815	1	2013-07-16 13:23:17	2013-07-16 13:23:17
-6818	protein_coding	21	11	5428733	5429749	-1	90711	ensembl	ANNOTATED	iron compound ABC transporter permease	1	6818	BTF1_27820	1	2013-07-16 13:36:45	2013-07-16 13:36:45
-6819	protein_coding	21	11	5429822	5430739	-1	90726	ensembl	ANNOTATED	iron compound ABC transporter substrate-binding protein	1	6819	BTF1_27825	1	2013-07-16 13:17:36	2013-07-16 13:17:36
-6820	protein_coding	21	11	5431071	5432120	1	90738	ensembl	ANNOTATED	thioredoxin reductase	1	6820	BTF1_27830	1	2013-07-16 13:07:40	2013-07-16 13:07:40
-6821	protein_coding	21	11	5432316	5432684	-1	90756	ensembl	ANNOTATED	hypothetical protein	1	6821	BTF1_27835	1	2013-07-16 13:06:47	2013-07-16 13:06:47
-6822	protein_coding	21	11	5432871	5433110	1	90765	ensembl	ANNOTATED	hypothetical protein	1	6822	BTF1_27840	1	2013-07-16 13:27:31	2013-07-16 13:27:31
-6823	protein_coding	21	11	5433235	5433348	1	90776	ensembl	ANNOTATED	hypothetical protein	1	6823	BTF1_27845	1	2013-07-16 13:33:42	2013-07-16 13:33:42
-6824	protein_coding	21	11	5433345	5433869	1	90785	ensembl	ANNOTATED	spore coat protein B	1	6824	BTF1_27850	1	2013-07-16 13:41:20	2013-07-16 13:41:20
-6825	protein_coding	21	11	5433890	5434339	1	90796	ensembl	ANNOTATED	spore coat protein B	1	6825	BTF1_27855	1	2013-07-16 13:07:14	2013-07-16 13:07:14
-6826	protein_coding	21	11	5434402	5434509	1	90806	ensembl	ANNOTATED	hypothetical protein	1	6826	BTF1_27860	1	2013-07-16 13:21:58	2013-07-16 13:21:58
-6827	protein_coding	21	11	5434502	5435170	1	90814	ensembl	ANNOTATED	hypothetical protein	1	6827	BTF1_27865	1	2013-07-16 13:17:03	2013-07-16 13:17:03
-6828	protein_coding	21	11	5435410	5436675	1	90824	ensembl	ANNOTATED	hypothetical protein	1	6828	BTF1_27870	1	2013-07-16 13:28:54	2013-07-16 13:28:54
-6829	protein_coding	21	11	5436813	5438039	1	90838	ensembl	ANNOTATED	sporulation kinase	1	6829	BTF1_27875	1	2013-07-16 13:25:02	2013-07-16 13:25:02
-6830	protein_coding	21	11	5438269	5438649	1	90861	ensembl	ANNOTATED	hypothetical protein	1	6830	BTF1_27880	1	2013-07-16 13:13:32	2013-07-16 13:13:32
-6831	protein_coding	21	11	5438784	5439416	-1	90869	ensembl	ANNOTATED	cyclase	1	6831	BTF1_27885	1	2013-07-16 13:39:09	2013-07-16 13:39:09
-6832	protein_coding	21	11	5439766	5440875	1	90878	ensembl	ANNOTATED	hypothetical protein	1	6832	BTF1_27890	1	2013-07-16 13:26:23	2013-07-16 13:26:23
-6833	protein_coding	21	11	5440987	5441769	1	90887	ensembl	ANNOTATED	hypothetical protein	1	6833	BTF1_27895	1	2013-07-16 13:38:43	2013-07-16 13:38:43
-6834	protein_coding	21	11	5441783	5443084	-1	90897	ensembl	ANNOTATED	benzoate transport protein	1	6834	BTF1_27900	1	2013-07-16 13:38:35	2013-07-16 13:38:35
-6835	protein_coding	21	11	5443231	5444757	-1	90913	ensembl	ANNOTATED	oxidoreductase	1	6835	BTF1_27905	1	2013-07-16 13:25:19	2013-07-16 13:25:19
-6836	protein_coding	21	11	5445339	5446424	1	90933	ensembl	ANNOTATED	fatty acid desaturase	1	6836	BTF1_27910	1	2013-07-16 13:29:55	2013-07-16 13:29:55
-6837	protein_coding	21	11	5446478	5447170	-1	90945	ensembl	ANNOTATED	amino acid ABC transporter permease	1	6837	BTF1_27915	1	2013-07-16 13:27:59	2013-07-16 13:27:59
-6838	protein_coding	21	11	5447281	5448075	-1	90962	ensembl	ANNOTATED	amino acid ABC transporter substrate-binding protein	1	6838	BTF1_27920	1	2013-07-16 13:42:24	2013-07-16 13:42:24
-6839	protein_coding	21	11	5448197	5448919	-1	90978	ensembl	ANNOTATED	amino acid ABC transporter ATP-binding protein	1	6839	BTF1_27925	1	2013-07-16 13:17:09	2013-07-16 13:17:09
-6840	protein_coding	21	11	5449130	5450422	1	90997	ensembl	ANNOTATED	methyl-accepting chemotaxis protein	1	6840	BTF1_27930	1	2013-07-16 13:23:58	2013-07-16 13:23:58
-6841	protein_coding	21	11	5450569	5451018	1	91012	ensembl	ANNOTATED	arginine repressor ArgR	1	6841	BTF1_27935	1	2013-07-16 13:21:31	2013-07-16 13:21:31
-6842	protein_coding	21	11	5451287	5452519	1	91040	ensembl	ANNOTATED	arginine deiminase	1	6842	BTF1_27940	1	2013-07-16 13:12:42	2013-07-16 13:12:42
-6843	protein_coding	21	11	5452550	5453548	1	91057	ensembl	ANNOTATED	ornithine carbamoyltransferase	1	6843	BTF1_27945	1	2013-07-16 13:40:34	2013-07-16 13:40:34
-6844	protein_coding	21	11	5453648	5455063	1	91077	ensembl	ANNOTATED	arginine/ornithine antiporter	1	6844	BTF1_27950	1	2013-07-16 13:29:37	2013-07-16 13:29:37
-6845	protein_coding	21	11	5455101	5456063	1	91097	ensembl	ANNOTATED	amino acid kinase	1	6845	BTF1_27955	1	2013-07-16 13:15:57	2013-07-16 13:15:57
-6846	protein_coding	21	11	5456265	5456954	1	91114	ensembl	ANNOTATED	Crp family transcriptional regulator	1	6846	BTF1_27960	1	2013-07-16 13:43:30	2013-07-16 13:43:30
-6847	protein_coding	21	11	5457111	5457794	1	91136	ensembl	ANNOTATED	hypothetical protein	1	6847	BTF1_27965	1	2013-07-16 13:24:27	2013-07-16 13:24:27
-6848	protein_coding	21	11	5457918	5459252	-1	91145	ensembl	ANNOTATED	FAD-dependent oxidase	1	6848	BTF1_27970	1	2013-07-16 13:29:36	2013-07-16 13:29:36
-6849	protein_coding	21	11	5459496	5461160	1	91163	ensembl	ANNOTATED	exo-alpha-1,4-glucosidase	1	6849	BTF1_27975	1	2013-07-16 13:39:41	2013-07-16 13:39:41
-6850	protein_coding	21	11	5461366	5463003	1	91184	ensembl	ANNOTATED	PTS system transporter subunit IICB	1	6850	BTF1_27980	1	2013-07-16 13:28:27	2013-07-16 13:28:27
-6851	protein_coding	21	11	5463008	5463799	1	91210	ensembl	ANNOTATED	exodeoxyribonuclease III	1	6851	BTF1_27985	1	2013-07-16 13:38:08	2013-07-16 13:38:08
-6852	protein_coding	21	11	5464105	5466966	1	91219	ensembl	ANNOTATED	phage infection protein	1	6852	BTF1_27990	1	2013-07-16 13:35:17	2013-07-16 13:35:17
-6853	protein_coding	21	11	5467007	5469196	-1	91230	ensembl	ANNOTATED	DNA topoisomerase III	1	6853	BTF1_27995	1	2013-07-16 13:14:36	2013-07-16 13:14:36
-6854	protein_coding	21	11	5469573	5470382	1	91257	ensembl	ANNOTATED	hydroxyethylthiazole kinase	1	6854	BTF1_28000	1	2013-07-16 13:16:51	2013-07-16 13:16:51
-6855	protein_coding	21	11	5470400	5471056	1	91277	ensembl	ANNOTATED	thiamine-phosphate pyrophosphorylase	1	6855	BTF1_28005	1	2013-07-16 13:28:09	2013-07-16 13:28:09
-6856	protein_coding	21	11	5471173	5472486	-1	91297	ensembl	ANNOTATED	anaerobic C4-dicarboxylate transporter	1	6856	BTF1_28010	1	2013-07-16 13:07:55	2013-07-16 13:07:55
-6857	protein_coding	21	11	5472987	5474729	1	91311	ensembl	ANNOTATED	methyl-accepting chemotaxis protein	1	6857	BTF1_28015	1	2013-07-16 13:11:53	2013-07-16 13:11:53
-6858	protein_coding	21	11	5474867	5478448	1	91329	ensembl	ANNOTATED	linear gramicidin synthetase subunit C	1	6858	BTF1_28020	1	2013-07-16 13:18:02	2013-07-16 13:18:02
-6859	protein_coding	21	11	5478704	5479024	1	91347	ensembl	ANNOTATED	hypothetical protein	1	6859	BTF1_28025	1	2013-07-16 13:13:54	2013-07-16 13:13:54
-6860	protein_coding	21	11	5478996	5479769	1	91358	ensembl	ANNOTATED	hydroxymethylpyrimidine transport system permease	1	6860	BTF1_28030	1	2013-07-16 13:42:57	2013-07-16 13:42:57
-6861	protein_coding	21	11	5479766	5480764	1	91373	ensembl	ANNOTATED	hydroxymethylpyrimidine-binding protein	1	6861	BTF1_28035	1	2013-07-16 13:19:08	2013-07-16 13:19:08
-6862	protein_coding	21	11	5480761	5481510	1	91386	ensembl	ANNOTATED	ABC transporter ATP-binding protein	1	6862	BTF1_28040	1	2013-07-16 13:32:58	2013-07-16 13:32:58
-6863	protein_coding	21	11	5481906	5483450	1	91405	ensembl	ANNOTATED	ABC transporter ATP-binding protein	1	6863	BTF1_28045	1	2013-07-16 13:32:53	2013-07-16 13:32:53
-6864	protein_coding	21	11	5483891	5485915	-1	91424	ensembl	ANNOTATED	chitinase B	1	6864	BTF1_28050	1	2013-07-16 13:41:04	2013-07-16 13:41:04
-6865	protein_coding	21	11	5486287	5486658	1	91450	ensembl	ANNOTATED	hypothetical protein	1	6865	BTF1_28055	1	2013-07-16 13:41:32	2013-07-16 13:41:32
-6866	protein_coding	21	11	5486669	5486983	1	91460	ensembl	ANNOTATED	hypothetical protein	1	6866	BTF1_28060	1	2013-07-16 13:11:32	2013-07-16 13:11:32
-6867	protein_coding	21	11	5486997	5487239	1	91472	ensembl	ANNOTATED	hypothetical protein	1	6867	BTF1_28065	1	2013-07-16 13:14:08	2013-07-16 13:14:08
-6868	protein_coding	21	11	5487365	5487508	1	91480	ensembl	ANNOTATED	hypothetical protein	1	6868	BTF1_28070	1	2013-07-16 13:12:04	2013-07-16 13:12:04
-6869	protein_coding	21	11	5487589	5488170	1	91489	ensembl	ANNOTATED	TetR family transcriptional regulator	1	6869	BTF1_28075	1	2013-07-16 13:21:11	2013-07-16 13:21:11
-6870	protein_coding	21	11	5488237	5489469	1	91510	ensembl	ANNOTATED	major facilitator family transporter	1	6870	BTF1_28080	1	2013-07-16 13:11:12	2013-07-16 13:11:12
-6871	protein_coding	21	11	5489583	5489777	1	91522	ensembl	ANNOTATED	DNA-binding protein	1	6871	BTF1_28085	1	2013-07-16 13:12:54	2013-07-16 13:12:54
-6872	protein_coding	21	11	5489847	5491130	-1	91534	ensembl	ANNOTATED	hypothetical protein	1	6872	BTF1_28090	1	2013-07-16 13:32:05	2013-07-16 13:32:05
-6873	protein_coding	21	11	5491239	5492552	-1	91546	ensembl	ANNOTATED	type I phosphodiesterase/nucleotide pyrophosphatase	1	6873	BTF1_28095	1	2013-07-16 13:20:17	2013-07-16 13:20:17
-6874	protein_coding	21	11	5492706	5492999	1	91560	ensembl	ANNOTATED	hypothetical protein	1	6874	BTF1_28100	1	2013-07-16 13:38:57	2013-07-16 13:38:57
-6875	protein_coding	21	11	5493350	5494780	1	91570	ensembl	ANNOTATED	prolyl-tRNA ligase	1	6875	BTF1_28105	1	2013-07-16 13:36:29	2013-07-16 13:36:29
-6876	protein_coding	21	11	5494895	315	-1	91593	ensembl	ANNOTATED	lpxtg-motif cell wall anchor domain-containing protein	1	6876	BTF1_00005	1	2013-07-16 13:43:36	2013-07-16 13:43:36
-6877	protein_coding	21	11	529	1407	1	91603	ensembl	ANNOTATED	ROK family protein	1	6877	BTF1_00010	1	2013-07-16 13:36:41	2013-07-16 13:36:41
-6878	protein_coding	21	11	1536	2132	1	91613	ensembl	ANNOTATED	Tellurium resistance protein terD/terE/terZ family	1	6878	BTF1_00015	1	2013-07-16 13:09:10	2013-07-16 13:09:10
-6879	protein_coding	21	11	2156	2740	1	91625	ensembl	ANNOTATED	tellurium resistance protein	1	6879	BTF1_00020	1	2013-07-16 13:08:16	2013-07-16 13:08:16
-6880	protein_coding	21	11	2826	3404	1	91637	ensembl	ANNOTATED	tellurium resistance protein	1	6880	BTF1_00025	1	2013-07-16 13:18:54	2013-07-16 13:18:54
-6881	protein_coding	21	11	3477	4268	1	91649	ensembl	ANNOTATED	tellurium resistance protein	1	6881	BTF1_00030	1	2013-07-16 13:37:12	2013-07-16 13:37:12
-6882	protein_coding	21	11	4378	6009	1	91661	ensembl	ANNOTATED	hypothetical protein	1	6882	BTF1_00035	1	2013-07-16 13:31:30	2013-07-16 13:31:30
-6883	protein_coding	21	11	6028	7110	1	91670	ensembl	ANNOTATED	Tellurite resistance protein	1	6883	BTF1_00040	1	2013-07-16 13:19:21	2013-07-16 13:19:21
-6884	protein_coding	21	11	7146	9812	-1	91680	ensembl	ANNOTATED	cation-transporting ATPase	1	6884	BTF1_00045	1	2013-07-16 13:24:54	2013-07-16 13:24:54
+6626	protein_coding	21	3	700	2754	-1	88455	ensembl		hypothetical protein	1	6626	BTF1_30582	1	2013-07-16 13:03:32	2013-07-16 13:03:32
+6627	protein_coding	21	3	2758	4539	-1	88463	ensembl		hypothetical protein	1	6627	BTF1_30587	1	2013-07-16 13:03:51	2013-07-16 13:03:51
+6628	protein_coding	21	3	4552	5766	-1	88472	ensembl		hypothetical protein	1	6628	BTF1_30592	1	2013-07-16 13:03:57	2013-07-16 13:03:57
+6629	protein_coding	21	3	5781	6728	-1	88480	ensembl		hypothetical protein	1	6629	BTF1_30597	1	2013-07-16 13:03:17	2013-07-16 13:03:17
+6630	protein_coding	21	3	6744	7493	-1	88488	ensembl		hypothetical protein	1	6630	BTF1_30602	1	2013-07-16 13:03:24	2013-07-16 13:03:24
+6631	protein_coding	21	3	7496	7870	-1	88496	ensembl		hypothetical protein	1	6631	BTF1_30607	1	2013-07-16 13:03:25	2013-07-16 13:03:25
+6632	protein_coding	21	3	7968	8195	-1	88504	ensembl		hypothetical protein	1	6632	BTF1_30612	1	2013-07-16 13:04:10	2013-07-16 13:04:10
+6633	protein_coding	21	3	8271	8933	-1	88512	ensembl		hypothetical protein	1	6633	BTF1_30617	1	2013-07-16 13:04:09	2013-07-16 13:04:09
+6634	protein_coding	21	3	230089	230622	1	88521	ensembl		hypothetical protein	1	6634	BTF1_31742	1	2013-07-16 13:03:54	2013-07-16 13:03:54
+6635	protein_coding	21	3	230700	230885	1	88529	ensembl		hypothetical protein	1	6635	BTF1_31747	1	2013-07-16 13:03:16	2013-07-16 13:03:16
+6636	protein_coding	21	3	230948	231418	1	88537	ensembl		hypothetical protein	1	6636	BTF1_31752	1	2013-07-16 13:03:37	2013-07-16 13:03:37
+6637	protein_coding	21	3	231603	231902	1	88545	ensembl		hypothetical protein	1	6637	BTF1_31757	1	2013-07-16 13:04:15	2013-07-16 13:04:15
+6638	protein_coding	21	3	232697	232912	1	88553	ensembl		hypothetical protein	1	6638	BTF1_31762	1	2013-07-16 13:03:31	2013-07-16 13:03:31
+6639	protein_coding	21	3	232927	233595	-1	88561	ensembl		hypothetical protein	1	6639	BTF1_31767	1	2013-07-16 13:04:11	2013-07-16 13:04:11
+6640	protein_coding	21	3	233785	233991	1	88569	ensembl		hypothetical protein	1	6640	BTF1_31772	1	2013-07-16 13:03:49	2013-07-16 13:03:49
+6641	protein_coding	21	3	234076	235323	-1	88577	ensembl		hypothetical protein	1	6641	BTF1_31777	1	2013-07-16 13:03:34	2013-07-16 13:03:34
+6642	protein_coding	21	3	235337	685	-1	88585	ensembl		hypothetical protein	1	6642	BTF1_30577	1	2013-07-16 13:03:58	2013-07-16 13:03:58
+6643	protein_coding	21	3	150202	151044	1	88594	ensembl		ThiF family protein	1	6643	BTF1_31212	1	2013-07-16 13:03:44	2013-07-16 13:03:44
+6644	protein_coding	21	3	151325	153892	1	88609	ensembl		hypothetical protein	1	6644	BTF1_31217	1	2013-07-16 13:04:07	2013-07-16 13:04:07
+6645	protein_coding	21	3	153966	154949	1	88618	ensembl		N-acetylmuramoyl-L-alanine amidase	1	6645	BTF1_31222	1	2013-07-16 13:04:11	2013-07-16 13:04:11
+6646	tRNA	28	3	155169	155243	1	88632	ensembl		\N	1	6646	BTF1_t31789	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6647	tRNA	28	3	155250	155329	1	88635	ensembl		\N	1	6647	BTF1_t31791	1	2013-07-16 13:04:16	2013-07-16 13:04:16
+6648	tRNA	28	3	155338	155425	1	88638	ensembl		\N	1	6648	BTF1_t31793	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6649	tRNA	28	3	155623	155697	1	88641	ensembl		\N	1	6649	BTF1_t31795	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6650	tRNA	28	3	155704	155775	1	88644	ensembl		\N	1	6650	BTF1_t31797	1	2013-07-16 13:04:18	2013-07-16 13:04:18
+6651	tRNA	28	3	155782	155854	1	88647	ensembl		\N	1	6651	BTF1_t31799	1	2013-07-16 13:04:18	2013-07-16 13:04:18
+6652	tRNA	28	3	156057	156133	1	88650	ensembl		\N	1	6652	BTF1_t31801	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6653	tRNA	28	3	156290	156363	1	88653	ensembl		\N	1	6653	BTF1_t31803	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6654	tRNA	28	3	156374	156448	1	88656	ensembl		\N	1	6654	BTF1_t31805	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6655	tRNA	28	3	156548	156621	1	88659	ensembl		\N	1	6655	BTF1_t31807	1	2013-07-16 13:04:16	2013-07-16 13:04:16
+6656	tRNA	28	3	156632	156705	1	88662	ensembl		\N	1	6656	BTF1_t31809	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6657	tRNA	28	3	156735	156807	1	88665	ensembl		\N	1	6657	BTF1_t31811	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6658	protein_coding	21	3	156856	157386	1	88668	ensembl		hypothetical protein	1	6658	BTF1_31227	1	2013-07-16 13:03:59	2013-07-16 13:03:59
+6659	tRNA	28	3	157418	157494	1	88676	ensembl		\N	1	6659	BTF1_t31813	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6660	tRNA	28	3	157503	157575	1	88679	ensembl		\N	1	6660	BTF1_t31815	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6661	tRNA	28	3	157852	157935	1	88682	ensembl		\N	1	6661	BTF1_t31817	1	2013-07-16 13:04:17	2013-07-16 13:04:17
+6662	tRNA	28	3	157939	158012	1	88685	ensembl		\N	1	6662	BTF1_t31819	1	2013-07-16 13:04:18	2013-07-16 13:04:18
+6663	tRNA	28	3	158104	158192	1	88688	ensembl		\N	1	6663	BTF1_t31821	1	2013-07-16 13:04:16	2013-07-16 13:04:16
+6664	protein_coding	21	3	158412	158852	1	88691	ensembl		hypothetical protein	1	6664	BTF1_31237	1	2013-07-16 13:04:12	2013-07-16 13:04:12
+6665	protein_coding	21	3	158878	159462	1	88700	ensembl		thymidine kinase	1	6665	BTF1_31242	1	2013-07-16 13:03:39	2013-07-16 13:03:39
+6666	protein_coding	21	3	159476	159976	1	88717	ensembl		hypothetical protein	1	6666	BTF1_31247	1	2013-07-16 13:03:17	2013-07-16 13:03:17
+6667	protein_coding	21	3	159997	160533	1	88726	ensembl		single-strand binding protein family	1	6667	BTF1_31252	1	2013-07-16 13:03:43	2013-07-16 13:03:43
+6668	protein_coding	21	4	210132	210989	1	88741	ensembl		hypothetical protein	1	6668	BTF1_32826	1	2013-07-16 13:04:34	2013-07-16 13:04:34
+6669	protein_coding	21	4	211116	212180	1	88749	ensembl		hypothetical protein	1	6669	BTF1_32831	1	2013-07-16 13:04:43	2013-07-16 13:04:43
+6670	protein_coding	21	4	212807	213178	1	88757	ensembl		hypothetical protein	1	6670	BTF1_32841	1	2013-07-16 13:04:52	2013-07-16 13:04:52
+6671	protein_coding	21	4	213615	213926	1	88765	ensembl		hypothetical protein	1	6671	BTF1_32846	1	2013-07-16 13:04:34	2013-07-16 13:04:34
+6672	protein_coding	21	4	213957	214370	1	88775	ensembl		hypothetical protein	1	6672	BTF1_32851	1	2013-07-16 13:05:04	2013-07-16 13:05:04
+6673	protein_coding	21	4	215358	215726	1	88788	ensembl		hypothetical protein	1	6673	BTF1_32856	1	2013-07-16 13:04:44	2013-07-16 13:04:44
+6674	protein_coding	21	4	215708	216049	1	88797	ensembl		hypothetical protein	1	6674	BTF1_32861	1	2013-07-16 13:04:33	2013-07-16 13:04:33
+6675	protein_coding	21	4	216280	217335	1	88805	ensembl		hypothetical protein	1	6675	BTF1_32866	1	2013-07-16 13:05:02	2013-07-16 13:05:02
+6676	protein_coding	21	4	217755	218327	1	88814	ensembl		hypothetical protein	1	6676	BTF1_32871	1	2013-07-16 13:05:03	2013-07-16 13:05:03
+6677	protein_coding	21	4	218689	219771	1	88823	ensembl		1-phosphatidylinositol phosphodiesterase	1	6677	BTF1_32876	1	2013-07-16 13:05:05	2013-07-16 13:05:05
+6678	protein_coding	21	4	220171	220830	-1	88838	ensembl		Hypothetical protein	1	6678	BTF1_32881	1	2013-07-16 13:04:36	2013-07-16 13:04:36
+6679	protein_coding	21	4	221204	221416	1	88852	ensembl		methionine-rich protein	1	6679	BTF1_32886	1	2013-07-16 13:04:24	2013-07-16 13:04:24
+6680	protein_coding	21	4	221988	222215	1	88861	ensembl		integrase protein	1	6680	BTF1_32891	1	2013-07-16 13:04:46	2013-07-16 13:04:46
+6681	protein_coding	21	4	222287	432	1	88879	ensembl		transposase Tn3	1	6681	BTF1_32896	1	2013-07-16 13:04:21	2013-07-16 13:04:21
+6682	protein_coding	21	4	572	1483	-1	88893	ensembl		crystal protein	1	6682	BTF1_31826	1	2013-07-16 13:04:22	2013-07-16 13:04:22
+6683	protein_coding	21	4	1640	2599	-1	88903	ensembl		crystal protein	1	6683	BTF1_31831	1	2013-07-16 13:04:31	2013-07-16 13:04:31
+6684	protein_coding	21	4	2873	3121	1	88914	ensembl		hypothetical protein	1	6684	BTF1_31836	1	2013-07-16 13:04:43	2013-07-16 13:04:43
+6685	protein_coding	21	4	3135	3731	1	88923	ensembl		insertion sequence IS240 protein	1	6685	BTF1_31841	1	2013-07-16 13:04:43	2013-07-16 13:04:43
+6686	protein_coding	21	4	3847	4158	-1	88937	ensembl		hypothetical protein	1	6686	BTF1_31846	1	2013-07-16 13:05:02	2013-07-16 13:05:02
+6687	protein_coding	21	4	4626	5060	-1	88946	ensembl		hypothetical protein	1	6687	BTF1_31851	1	2013-07-16 13:04:38	2013-07-16 13:04:38
+6688	protein_coding	21	4	5444	6019	-1	88954	ensembl		hypothetical protein	1	6688	BTF1_31856	1	2013-07-16 13:04:53	2013-07-16 13:04:53
+6689	protein_coding	21	4	7087	8286	-1	88963	ensembl		major facilitator superfamily protein	1	6689	BTF1_31871	1	2013-07-16 13:04:41	2013-07-16 13:04:41
+6690	protein_coding	21	4	8316	8516	-1	88978	ensembl		IS4 family transposase	1	6690	BTF1_31876	1	2013-07-16 13:05:05	2013-07-16 13:05:05
+6691	protein_coding	21	4	8683	8943	-1	88986	ensembl		hypothetical protein	1	6691	BTF1_31881	1	2013-07-16 13:05:01	2013-07-16 13:05:01
+6692	protein_coding	21	4	9011	10948	-1	88994	ensembl		hypothetical protein	1	6692	BTF1_31886	1	2013-07-16 13:04:45	2013-07-16 13:04:45
+6693	protein_coding	21	7	347058	347492	-1	89002	ensembl		hypothetical protein	1	6693	BTF1_30562	1	2013-07-16 13:05:41	2013-07-16 13:05:41
+6694	protein_coding	21	7	347641	348741	-1	89010	ensembl		hypothetical protein	1	6694	BTF1_30567	1	2013-07-16 13:06:06	2013-07-16 13:06:06
+6695	protein_coding	21	7	348754	349407	-1	89018	ensembl		hypothetical protein	1	6695	BTF1_30572	1	2013-07-16 13:06:29	2013-07-16 13:06:29
+6696	protein_coding	21	7	349459	333	-1	89026	ensembl		hypothetical protein	1	6696	BTF1_28407	1	2013-07-16 13:06:14	2013-07-16 13:06:14
+6697	protein_coding	21	7	453	1598	-1	89034	ensembl		hypothetical protein	1	6697	BTF1_28412	1	2013-07-16 13:06:04	2013-07-16 13:06:04
+6698	protein_coding	21	7	1612	1947	-1	89042	ensembl		hypothetical protein	1	6698	BTF1_28417	1	2013-07-16 13:05:49	2013-07-16 13:05:49
+6699	protein_coding	21	7	2425	2937	-1	89050	ensembl		hypothetical protein	1	6699	BTF1_28422	1	2013-07-16 13:05:26	2013-07-16 13:05:26
+6700	protein_coding	21	7	2957	3427	-1	89058	ensembl		hypothetical protein	1	6700	BTF1_28427	1	2013-07-16 13:05:35	2013-07-16 13:05:35
+6701	protein_coding	21	7	3458	3892	-1	89066	ensembl		hypothetical protein	1	6701	BTF1_28432	1	2013-07-16 13:05:15	2013-07-16 13:05:15
+6702	protein_coding	21	7	4042	4494	-1	89074	ensembl		hypothetical protein	1	6702	BTF1_28437	1	2013-07-16 13:05:33	2013-07-16 13:05:33
+6703	protein_coding	21	7	4528	4965	-1	89082	ensembl		hypothetical protein	1	6703	BTF1_28442	1	2013-07-16 13:05:38	2013-07-16 13:05:38
+6704	protein_coding	21	11	5300113	5300397	1	89090	ensembl		hypothetical protein	1	6704	BTF1_27315	1	2013-07-16 13:09:18	2013-07-16 13:09:18
+6705	protein_coding	21	11	5300922	5301548	1	89098	ensembl		hypothetical protein	1	6705	BTF1_27320	1	2013-07-16 13:31:48	2013-07-16 13:31:48
+6706	protein_coding	21	11	5301578	5302180	1	89107	ensembl		putative prophage LambdaBa01, prohead protease	1	6706	BTF1_27325	1	2013-07-16 13:25:20	2013-07-16 13:25:20
+6707	protein_coding	21	11	5302408	5303115	1	89120	ensembl		hypothetical protein	1	6707	BTF1_27330	1	2013-07-16 13:12:50	2013-07-16 13:12:50
+6708	protein_coding	21	11	5303151	5304335	1	89129	ensembl		putative DNA-binding protein	1	6708	BTF1_27335	1	2013-07-16 13:15:34	2013-07-16 13:15:34
+6709	protein_coding	21	11	5304508	5305038	-1	89142	ensembl		hypothetical protein	1	6709	BTF1_27340	1	2013-07-16 13:36:54	2013-07-16 13:36:54
+6710	protein_coding	21	11	5305053	5306660	-1	89151	ensembl		hypothetical protein	1	6710	BTF1_27345	1	2013-07-16 13:29:49	2013-07-16 13:29:49
+6711	protein_coding	21	11	5306860	5307246	1	89165	ensembl		putative prophage LambdaBa04, DNA binding protein	1	6711	BTF1_27350	1	2013-07-16 13:24:02	2013-07-16 13:24:02
+6712	protein_coding	21	11	5308066	5309604	1	89175	ensembl		GMP synthase	1	6712	BTF1_27355	1	2013-07-16 13:09:04	2013-07-16 13:09:04
+6713	protein_coding	21	11	5309909	5310424	1	89204	ensembl		hypothetical protein	1	6713	BTF1_27360	1	2013-07-16 13:30:56	2013-07-16 13:30:56
+6714	protein_coding	21	11	5310421	5311137	1	89212	ensembl		hypothetical protein	1	6714	BTF1_27365	1	2013-07-16 13:26:15	2013-07-16 13:26:15
+6715	protein_coding	21	11	5311140	5312159	1	89220	ensembl		hypothetical protein	1	6715	BTF1_27370	1	2013-07-16 13:07:13	2013-07-16 13:07:13
+6716	protein_coding	21	11	5312477	5312884	1	89228	ensembl		hypothetical protein	1	6716	BTF1_27375	1	2013-07-16 13:40:17	2013-07-16 13:40:17
+6717	protein_coding	21	11	5313273	5313545	1	89236	ensembl		hypothetical protein	1	6717	BTF1_27380	1	2013-07-16 13:37:40	2013-07-16 13:37:40
+6718	protein_coding	21	11	5313814	5315220	1	89245	ensembl		FtsK/SpoIIIE family protein	1	6718	BTF1_27385	1	2013-07-16 13:39:16	2013-07-16 13:39:16
+6719	protein_coding	21	11	5315514	5316017	1	89267	ensembl		hypothetical protein	1	6719	BTF1_27390	1	2013-07-16 13:14:28	2013-07-16 13:14:28
+6720	protein_coding	21	11	5315998	5317026	1	89276	ensembl		replication initiation factor	1	6720	BTF1_27395	1	2013-07-16 13:08:35	2013-07-16 13:08:35
+6721	protein_coding	21	11	5317047	5317253	1	89291	ensembl		hypothetical protein	1	6721	BTF1_27400	1	2013-07-16 13:38:43	2013-07-16 13:38:43
+6722	protein_coding	21	11	5317250	5318503	1	89301	ensembl		integrase family protein	1	6722	BTF1_27405	1	2013-07-16 13:29:35	2013-07-16 13:29:35
+6723	protein_coding	21	11	5318504	5319310	1	89320	ensembl		serine/threonine protein phosphatase	1	6723	BTF1_27410	1	2013-07-16 13:09:02	2013-07-16 13:09:02
+6724	protein_coding	21	11	5319297	5319689	1	89332	ensembl		hypothetical protein	1	6724	BTF1_27415	1	2013-07-16 13:42:07	2013-07-16 13:42:07
+6725	protein_coding	21	11	5320179	5321504	1	89341	ensembl		xanthine/uracil permease	1	6725	BTF1_27420	1	2013-07-16 13:12:33	2013-07-16 13:12:33
+6726	protein_coding	21	11	5321798	5322499	1	89358	ensembl		two-component response regulator	1	6726	BTF1_27425	1	2013-07-16 13:43:11	2013-07-16 13:43:11
+6727	protein_coding	21	11	5322483	5323988	1	89379	ensembl		two component system histidine kinase	1	6727	BTF1_27430	1	2013-07-16 13:23:41	2013-07-16 13:23:41
+6728	rRNA	28	11	5324281	5325843	1	89401	ensembl		\N	1	6728	BTF1_r28371	1	2013-07-16 13:44:01	2013-07-16 13:44:01
+6729	rRNA	28	11	5325982	5328906	1	89404	ensembl		\N	1	6729	BTF1_r28399	1	2013-07-16 13:43:58	2013-07-16 13:43:58
+6730	rRNA	28	11	5328953	5329068	1	89407	ensembl		\N	1	6730	BTF1_r28343	1	2013-07-16 13:44:00	2013-07-16 13:44:00
+6731	protein_coding	21	11	5329301	5330260	1	89411	ensembl		alpha/beta hydrolase	1	6731	BTF1_27435	1	2013-07-16 13:36:53	2013-07-16 13:36:53
+6732	protein_coding	21	11	5330461	5331192	1	89423	ensembl		FrnE protein	1	6732	BTF1_27440	1	2013-07-16 13:38:09	2013-07-16 13:38:09
+6733	rRNA	28	11	5331540	5333102	1	89435	ensembl		\N	1	6733	BTF1_r28373	1	2013-07-16 13:43:54	2013-07-16 13:43:54
+6734	rRNA	28	11	5333241	5336165	1	89438	ensembl		\N	1	6734	BTF1_r28401	1	2013-07-16 13:43:54	2013-07-16 13:43:54
+6735	rRNA	28	11	5336211	5336326	1	89441	ensembl		\N	1	6735	BTF1_r28345	1	2013-07-16 13:43:59	2013-07-16 13:43:59
+6736	protein_coding	21	11	5336495	5336923	-1	89445	ensembl		GntR family transcriptional regulator	1	6736	BTF1_27445	1	2013-07-16 13:15:40	2013-07-16 13:15:40
+6737	rRNA	28	11	5339054	5340616	1	89461	ensembl		\N	1	6737	BTF1_r28375	1	2013-07-16 13:43:55	2013-07-16 13:43:55
+6738	rRNA	28	11	5340755	5343679	1	89464	ensembl		\N	1	6738	BTF1_r28403	1	2013-07-16 13:43:53	2013-07-16 13:43:53
+6739	rRNA	28	11	5343725	5343840	1	89467	ensembl		\N	1	6739	BTF1_r28347	1	2013-07-16 13:43:57	2013-07-16 13:43:57
+6740	protein_coding	21	11	5343916	5344374	-1	89470	ensembl		asch domain superfamily protein	1	6740	BTF1_27460	1	2013-07-16 13:15:03	2013-07-16 13:15:03
+6741	protein_coding	21	11	5344731	5345528	-1	89482	ensembl		undecaprenyl pyrophosphate phosphatase	1	6741	BTF1_27465	1	2013-07-16 13:29:26	2013-07-16 13:29:26
+6742	protein_coding	21	11	5345546	5346283	-1	89505	ensembl		bacitracin ABC transporter permease	1	6742	BTF1_27470	1	2013-07-16 13:34:14	2013-07-16 13:34:14
+6743	protein_coding	21	11	5346276	5347205	-1	89514	ensembl		bacitracin ABC transporter ATP-binding protein	1	6743	BTF1_27475	1	2013-07-16 13:27:09	2013-07-16 13:27:09
+6744	protein_coding	21	11	5347274	5348287	-1	89533	ensembl		sensor histidine kinase	1	6744	BTF1_27480	1	2013-07-16 13:20:05	2013-07-16 13:20:05
+6745	protein_coding	21	11	5348277	5348990	-1	89557	ensembl		DNA-binding response regulator	1	6745	BTF1_27485	1	2013-07-16 13:33:30	2013-07-16 13:33:30
+6746	rRNA	28	11	5349468	5351030	1	89577	ensembl		\N	1	6746	BTF1_r28377	1	2013-07-16 13:43:53	2013-07-16 13:43:53
+6747	rRNA	28	11	5351169	5354093	1	89580	ensembl		\N	1	6747	BTF1_r28405	1	2013-07-16 13:43:54	2013-07-16 13:43:54
+6748	rRNA	28	11	5354139	5354254	1	89583	ensembl		\N	1	6748	BTF1_r28349	1	2013-07-16 13:43:58	2013-07-16 13:43:58
+6749	protein_coding	21	11	5354467	5355387	1	89587	ensembl		transporter Drug/Metabolite Exporter family protein	1	6749	BTF1_27490	1	2013-07-16 13:23:57	2013-07-16 13:23:57
+6750	protein_coding	21	11	5355474	5356265	-1	89599	ensembl		hypothetical protein	1	6750	BTF1_27495	1	2013-07-16 13:21:59	2013-07-16 13:21:59
+6751	rRNA	28	11	5356579	5358141	1	89612	ensembl		\N	1	6751	BTF1_r28379	1	2013-07-16 13:43:53	2013-07-16 13:43:53
+6752	rRNA	28	11	5358280	5361204	1	89615	ensembl		\N	1	6752	BTF1_r28407	1	2013-07-16 13:43:53	2013-07-16 13:43:53
+6753	rRNA	28	11	5361251	5361366	1	89618	ensembl		\N	1	6753	BTF1_r28351	1	2013-07-16 13:43:55	2013-07-16 13:43:55
+6754	protein_coding	21	11	5362106	5362591	1	89622	ensembl		phosphoribosylaminoimidazole carboxylase catalytic subunit	1	6754	BTF1_27500	1	2013-07-16 13:12:36	2013-07-16 13:12:36
+6755	protein_coding	21	11	5362588	5363739	1	89637	ensembl		phosphoribosylaminoimidazole carboxylase ATPase subunit	1	6755	BTF1_27505	1	2013-07-16 13:07:35	2013-07-16 13:07:35
+6756	protein_coding	21	11	5363736	5365043	1	89666	ensembl		adenylosuccinate lyase	1	6756	BTF1_27510	1	2013-07-16 13:17:58	2013-07-16 13:17:58
+6757	protein_coding	21	11	5365132	5365851	1	89689	ensembl		phosphoribosylaminoimidazole-succinocarboxamide synthase	1	6757	BTF1_27515	1	2013-07-16 13:14:58	2013-07-16 13:14:58
+6758	protein_coding	21	11	5365844	5366098	1	89707	ensembl		phosphoribosylformylglycinamidine synthase subunit PurS	1	6758	BTF1_27520	1	2013-07-16 13:12:48	2013-07-16 13:12:48
+6759	protein_coding	21	11	5366095	5366778	1	89719	ensembl		phosphoribosylformylglycinamidine synthase I	1	6759	BTF1_27525	1	2013-07-16 13:20:46	2013-07-16 13:20:46
+6760	protein_coding	21	11	5366762	5368981	1	89740	ensembl		phosphoribosylformylglycinamidine synthase II	1	6760	BTF1_27530	1	2013-07-16 13:29:17	2013-07-16 13:29:17
+6761	protein_coding	21	11	5368966	5370381	1	89761	ensembl		amidophosphoribosyltransferase	1	6761	BTF1_27535	1	2013-07-16 13:10:58	2013-07-16 13:10:58
+6762	protein_coding	21	11	5370487	5371527	1	89784	ensembl		phosphoribosylaminoimidazole synthetase	1	6762	BTF1_27540	1	2013-07-16 13:36:20	2013-07-16 13:36:20
+6763	protein_coding	21	11	5371524	5372111	1	89805	ensembl		phosphoribosylglycinamide formyltransferase	1	6763	BTF1_27545	1	2013-07-16 13:23:37	2013-07-16 13:23:37
+6764	protein_coding	21	11	5372136	5373671	1	89825	ensembl		bifunctional phosphoribosylaminoimidazolecarboxamide formyltransferase/IMP cyclohydrolase	1	6764	BTF1_27550	1	2013-07-16 13:40:41	2013-07-16 13:40:41
+6765	protein_coding	21	11	5374051	5375322	1	89844	ensembl		phosphoribosylamine--glycine ligase	1	6765	BTF1_27555	1	2013-07-16 13:22:35	2013-07-16 13:22:35
+6766	protein_coding	21	11	5375359	5375523	-1	89875	ensembl		hypothetical protein	1	6766	BTF1_27560	1	2013-07-16 13:41:32	2013-07-16 13:41:32
+6767	protein_coding	21	11	5375539	5376384	-1	89889	ensembl		hypothetical protein	1	6767	BTF1_27565	1	2013-07-16 13:27:17	2013-07-16 13:27:17
+6768	protein_coding	21	11	5376603	5376980	-1	89901	ensembl		hypothetical protein	1	6768	BTF1_27570	1	2013-07-16 13:42:21	2013-07-16 13:42:21
+6769	protein_coding	21	11	5377262	5377951	1	89911	ensembl		geranylgeranylglyceryl phosphate synthase-like protein	1	6769	BTF1_27575	1	2013-07-16 13:41:32	2013-07-16 13:41:32
+6770	protein_coding	21	11	5377952	5380213	1	89927	ensembl		ATP-dependent DNA helicase PcrA	1	6770	BTF1_27580	1	2013-07-16 13:30:44	2013-07-16 13:30:44
+6771	protein_coding	21	11	5380228	5382237	1	89952	ensembl		NAD-dependent DNA ligase LigA	1	6771	BTF1_27585	1	2013-07-16 13:16:58	2013-07-16 13:16:58
+6772	protein_coding	21	11	5382254	5383447	1	89980	ensembl		lipoprotein	1	6772	BTF1_27590	1	2013-07-16 13:26:19	2013-07-16 13:26:19
+6773	protein_coding	21	11	5383544	5384314	1	89990	ensembl		hypothetical protein	1	6773	BTF1_27595	1	2013-07-16 13:34:50	2013-07-16 13:34:50
+6774	protein_coding	21	11	5384468	5386015	1	90002	ensembl		1-pyrroline-5-carboxylate dehydrogenase	1	6774	BTF1_27600	1	2013-07-16 13:22:13	2013-07-16 13:22:13
+6775	protein_coding	21	11	5386286	5386831	-1	90027	ensembl		isochorismatase	1	6775	BTF1_27605	1	2013-07-16 13:38:42	2013-07-16 13:38:42
+6776	protein_coding	21	11	5387304	5388323	1	90039	ensembl		ABC transporter ATP-binding protein	1	6776	BTF1_27610	1	2013-07-16 13:25:57	2013-07-16 13:25:57
+6777	protein_coding	21	11	5388313	5388978	1	90065	ensembl		ABC transporter permease	1	6777	BTF1_27615	1	2013-07-16 13:08:07	2013-07-16 13:08:07
+6778	protein_coding	21	11	5389000	5389854	1	90080	ensembl		ABC transporter substrate-binding protein	1	6778	BTF1_27620	1	2013-07-16 13:22:04	2013-07-16 13:22:04
+6779	protein_coding	21	11	5390022	5390492	-1	90089	ensembl		hypothetical protein	1	6779	BTF1_27625	1	2013-07-16 13:25:05	2013-07-16 13:25:05
+6780	protein_coding	21	11	5390551	5390742	-1	90098	ensembl		hypothetical protein	1	6780	BTF1_27630	1	2013-07-16 13:06:45	2013-07-16 13:06:45
+6781	protein_coding	21	11	5390735	5391913	-1	90108	ensembl		anion-transporting ATPase	1	6781	BTF1_27635	1	2013-07-16 13:27:19	2013-07-16 13:27:19
+6782	protein_coding	21	11	5391992	5392474	-1	90126	ensembl		transcriptional regulator, MarR family protein	1	6782	BTF1_27640	1	2013-07-16 13:07:33	2013-07-16 13:07:33
+6783	protein_coding	21	11	5392706	5392942	1	90144	ensembl		hypothetical protein	1	6783	BTF1_27645	1	2013-07-16 13:23:54	2013-07-16 13:23:54
+6784	protein_coding	21	11	5393084	5393374	1	90154	ensembl		asparaginyl/glutamyl-tRNA amidotransferase subunit C	1	6784	BTF1_27650	1	2013-07-16 13:30:18	2013-07-16 13:30:18
+6785	protein_coding	21	11	5393390	5394847	1	90174	ensembl		aspartyl/glutamyl-tRNA amidotransferase subunit A	1	6785	BTF1_27655	1	2013-07-16 13:37:11	2013-07-16 13:37:11
+6786	protein_coding	21	11	5394862	5396289	1	90195	ensembl		aspartyl/glutamyl-tRNA amidotransferase subunit B	1	6786	BTF1_27660	1	2013-07-16 13:41:02	2013-07-16 13:41:02
+6787	protein_coding	21	11	5396850	5397755	1	90218	ensembl		lipid kinase	1	6787	BTF1_27665	1	2013-07-16 13:28:06	2013-07-16 13:28:06
+6788	protein_coding	21	11	5397896	5398642	1	90236	ensembl		haloacid dehalogenase/epoxide hydrolase	1	6788	BTF1_27670	1	2013-07-16 13:22:11	2013-07-16 13:22:11
+6789	protein_coding	21	11	5398797	5400161	1	90249	ensembl		4-aminobutyrate aminotransferase	1	6789	BTF1_27675	1	2013-07-16 13:20:01	2013-07-16 13:20:01
+6790	protein_coding	21	11	5400277	5401644	1	90269	ensembl		sigma-54-dependent transcriptional activator	1	6790	BTF1_27680	1	2013-07-16 13:22:46	2013-07-16 13:22:46
+6791	protein_coding	21	11	5401637	5403088	1	90301	ensembl		succinate-semialdehyde dehydrogenase	1	6791	BTF1_27685	1	2013-07-16 13:14:19	2013-07-16 13:14:19
+6792	protein_coding	21	11	5403136	5403459	1	90320	ensembl		quaternary ammonium	1	6792	BTF1_27690	1	2013-07-16 13:39:21	2013-07-16 13:39:21
+6793	protein_coding	21	11	5403592	5404083	1	90336	ensembl		hypothetical protein	1	6793	BTF1_27695	1	2013-07-16 13:09:08	2013-07-16 13:09:08
+6794	protein_coding	21	11	5404128	5405357	-1	90348	ensembl		aminopeptidase	1	6794	BTF1_27700	1	2013-07-16 13:26:05	2013-07-16 13:26:05
+6795	protein_coding	21	11	5405474	5406556	-1	90362	ensembl		polysaccharide deacetylase-like protein	1	6795	BTF1_27705	1	2013-07-16 13:41:01	2013-07-16 13:41:01
+6796	protein_coding	21	11	5406704	5406877	-1	90377	ensembl		hypothetical protein	1	6796	BTF1_27710	1	2013-07-16 13:35:08	2013-07-16 13:35:08
+6797	protein_coding	21	11	5407094	5407801	1	90385	ensembl		hypothetical protein	1	6797	BTF1_27715	1	2013-07-16 13:20:00	2013-07-16 13:20:00
+6798	protein_coding	21	11	5407848	5409044	-1	90394	ensembl		nucleoside permease nupC	1	6798	BTF1_27720	1	2013-07-16 13:41:35	2013-07-16 13:41:35
+6799	protein_coding	21	11	5409470	5410846	1	90413	ensembl		tRNA (Uracil-5-)-methyltransferase	1	6799	BTF1_27725	1	2013-07-16 13:36:03	2013-07-16 13:36:03
+6800	protein_coding	21	11	5411007	5411996	1	90435	ensembl		tRNA-dihydrouridine synthase	1	6800	BTF1_27730	1	2013-07-16 13:34:39	2013-07-16 13:34:39
+6801	protein_coding	21	11	5412348	5412866	1	90453	ensembl		hypothetical protein	1	6801	BTF1_27735	1	2013-07-16 13:08:22	2013-07-16 13:08:22
+6802	protein_coding	21	11	5412961	5413668	1	90463	ensembl		zinc metalloprotease	1	6802	BTF1_27740	1	2013-07-16 13:35:51	2013-07-16 13:35:51
+6803	protein_coding	21	11	5413665	5413856	-1	90476	ensembl		hypothetical protein	1	6803	BTF1_27745	1	2013-07-16 13:22:27	2013-07-16 13:22:27
+6804	protein_coding	21	11	5413888	5414583	-1	90485	ensembl		hypothetical protein	1	6804	BTF1_27750	1	2013-07-16 13:24:02	2013-07-16 13:24:02
+6805	protein_coding	21	11	5414598	5415707	-1	90498	ensembl		mandelate racemase/muconate lactonizing protein	1	6805	BTF1_27755	1	2013-07-16 13:25:27	2013-07-16 13:25:27
+6806	protein_coding	21	11	5415801	5417072	1	90511	ensembl		transcriptional regulator domain-containing protein	1	6806	BTF1_27760	1	2013-07-16 13:35:40	2013-07-16 13:35:40
+6807	protein_coding	21	11	5417061	5418482	-1	90520	ensembl		Na+/H+ antiporter NhaC	1	6807	BTF1_27765	1	2013-07-16 13:42:40	2013-07-16 13:42:40
+6808	protein_coding	21	11	5418775	5419890	1	90535	ensembl		amidohydrolase	1	6808	BTF1_27770	1	2013-07-16 13:36:58	2013-07-16 13:36:58
+6809	protein_coding	21	11	5420084	5420689	1	90548	ensembl		hypothetical protein	1	6809	BTF1_27775	1	2013-07-16 13:38:34	2013-07-16 13:38:34
+6810	protein_coding	21	11	5420722	5422248	-1	90557	ensembl		alkyl hydroperoxide reductase subunit F	1	6810	BTF1_27780	1	2013-07-16 13:19:13	2013-07-16 13:19:13
+6811	protein_coding	21	11	5422263	5422826	-1	90588	ensembl		Alkyl hydroperoxide reductase C22	1	6811	BTF1_27785	1	2013-07-16 13:18:31	2013-07-16 13:18:31
+6812	protein_coding	21	11	5423418	5424647	1	90608	ensembl		5-methylribose kinase	1	6812	BTF1_27790	1	2013-07-16 13:25:47	2013-07-16 13:25:47
+6813	protein_coding	21	11	5424657	5425703	1	90628	ensembl		methylthioribose-1-phosphate isomerase	1	6813	BTF1_27795	1	2013-07-16 13:21:46	2013-07-16 13:21:46
+6814	protein_coding	21	11	5425757	5426398	1	90647	ensembl		L-fuculose phosphate aldolase	1	6814	BTF1_27800	1	2013-07-16 13:37:42	2013-07-16 13:37:42
+6815	protein_coding	21	11	5426463	5427347	-1	90661	ensembl		integrase core domain-containing protein	1	6815	BTF1_27805	1	2013-07-16 13:18:06	2013-07-16 13:18:06
+6816	protein_coding	21	11	5427314	5427619	-1	90677	ensembl		transposase	1	6816	BTF1_27810	1	2013-07-16 13:17:04	2013-07-16 13:17:04
+6817	protein_coding	21	11	5427729	5428736	-1	90694	ensembl		iron compound ABC transporter permease	1	6817	BTF1_27815	1	2013-07-16 13:23:17	2013-07-16 13:23:17
+6818	protein_coding	21	11	5428733	5429749	-1	90711	ensembl		iron compound ABC transporter permease	1	6818	BTF1_27820	1	2013-07-16 13:36:45	2013-07-16 13:36:45
+6819	protein_coding	21	11	5429822	5430739	-1	90726	ensembl		iron compound ABC transporter substrate-binding protein	1	6819	BTF1_27825	1	2013-07-16 13:17:36	2013-07-16 13:17:36
+6820	protein_coding	21	11	5431071	5432120	1	90738	ensembl		thioredoxin reductase	1	6820	BTF1_27830	1	2013-07-16 13:07:40	2013-07-16 13:07:40
+6821	protein_coding	21	11	5432316	5432684	-1	90756	ensembl		hypothetical protein	1	6821	BTF1_27835	1	2013-07-16 13:06:47	2013-07-16 13:06:47
+6822	protein_coding	21	11	5432871	5433110	1	90765	ensembl		hypothetical protein	1	6822	BTF1_27840	1	2013-07-16 13:27:31	2013-07-16 13:27:31
+6823	protein_coding	21	11	5433235	5433348	1	90776	ensembl		hypothetical protein	1	6823	BTF1_27845	1	2013-07-16 13:33:42	2013-07-16 13:33:42
+6824	protein_coding	21	11	5433345	5433869	1	90785	ensembl		spore coat protein B	1	6824	BTF1_27850	1	2013-07-16 13:41:20	2013-07-16 13:41:20
+6825	protein_coding	21	11	5433890	5434339	1	90796	ensembl		spore coat protein B	1	6825	BTF1_27855	1	2013-07-16 13:07:14	2013-07-16 13:07:14
+6826	protein_coding	21	11	5434402	5434509	1	90806	ensembl		hypothetical protein	1	6826	BTF1_27860	1	2013-07-16 13:21:58	2013-07-16 13:21:58
+6827	protein_coding	21	11	5434502	5435170	1	90814	ensembl		hypothetical protein	1	6827	BTF1_27865	1	2013-07-16 13:17:03	2013-07-16 13:17:03
+6828	protein_coding	21	11	5435410	5436675	1	90824	ensembl		hypothetical protein	1	6828	BTF1_27870	1	2013-07-16 13:28:54	2013-07-16 13:28:54
+6829	protein_coding	21	11	5436813	5438039	1	90838	ensembl		sporulation kinase	1	6829	BTF1_27875	1	2013-07-16 13:25:02	2013-07-16 13:25:02
+6830	protein_coding	21	11	5438269	5438649	1	90861	ensembl		hypothetical protein	1	6830	BTF1_27880	1	2013-07-16 13:13:32	2013-07-16 13:13:32
+6831	protein_coding	21	11	5438784	5439416	-1	90869	ensembl		cyclase	1	6831	BTF1_27885	1	2013-07-16 13:39:09	2013-07-16 13:39:09
+6832	protein_coding	21	11	5439766	5440875	1	90878	ensembl		hypothetical protein	1	6832	BTF1_27890	1	2013-07-16 13:26:23	2013-07-16 13:26:23
+6833	protein_coding	21	11	5440987	5441769	1	90887	ensembl		hypothetical protein	1	6833	BTF1_27895	1	2013-07-16 13:38:43	2013-07-16 13:38:43
+6834	protein_coding	21	11	5441783	5443084	-1	90897	ensembl		benzoate transport protein	1	6834	BTF1_27900	1	2013-07-16 13:38:35	2013-07-16 13:38:35
+6835	protein_coding	21	11	5443231	5444757	-1	90913	ensembl		oxidoreductase	1	6835	BTF1_27905	1	2013-07-16 13:25:19	2013-07-16 13:25:19
+6836	protein_coding	21	11	5445339	5446424	1	90933	ensembl		fatty acid desaturase	1	6836	BTF1_27910	1	2013-07-16 13:29:55	2013-07-16 13:29:55
+6837	protein_coding	21	11	5446478	5447170	-1	90945	ensembl		amino acid ABC transporter permease	1	6837	BTF1_27915	1	2013-07-16 13:27:59	2013-07-16 13:27:59
+6838	protein_coding	21	11	5447281	5448075	-1	90962	ensembl		amino acid ABC transporter substrate-binding protein	1	6838	BTF1_27920	1	2013-07-16 13:42:24	2013-07-16 13:42:24
+6839	protein_coding	21	11	5448197	5448919	-1	90978	ensembl		amino acid ABC transporter ATP-binding protein	1	6839	BTF1_27925	1	2013-07-16 13:17:09	2013-07-16 13:17:09
+6840	protein_coding	21	11	5449130	5450422	1	90997	ensembl		methyl-accepting chemotaxis protein	1	6840	BTF1_27930	1	2013-07-16 13:23:58	2013-07-16 13:23:58
+6841	protein_coding	21	11	5450569	5451018	1	91012	ensembl		arginine repressor ArgR	1	6841	BTF1_27935	1	2013-07-16 13:21:31	2013-07-16 13:21:31
+6842	protein_coding	21	11	5451287	5452519	1	91040	ensembl		arginine deiminase	1	6842	BTF1_27940	1	2013-07-16 13:12:42	2013-07-16 13:12:42
+6843	protein_coding	21	11	5452550	5453548	1	91057	ensembl		ornithine carbamoyltransferase	1	6843	BTF1_27945	1	2013-07-16 13:40:34	2013-07-16 13:40:34
+6844	protein_coding	21	11	5453648	5455063	1	91077	ensembl		arginine/ornithine antiporter	1	6844	BTF1_27950	1	2013-07-16 13:29:37	2013-07-16 13:29:37
+6845	protein_coding	21	11	5455101	5456063	1	91097	ensembl		amino acid kinase	1	6845	BTF1_27955	1	2013-07-16 13:15:57	2013-07-16 13:15:57
+6846	protein_coding	21	11	5456265	5456954	1	91114	ensembl		Crp family transcriptional regulator	1	6846	BTF1_27960	1	2013-07-16 13:43:30	2013-07-16 13:43:30
+6847	protein_coding	21	11	5457111	5457794	1	91136	ensembl		hypothetical protein	1	6847	BTF1_27965	1	2013-07-16 13:24:27	2013-07-16 13:24:27
+6848	protein_coding	21	11	5457918	5459252	-1	91145	ensembl		FAD-dependent oxidase	1	6848	BTF1_27970	1	2013-07-16 13:29:36	2013-07-16 13:29:36
+6849	protein_coding	21	11	5459496	5461160	1	91163	ensembl		exo-alpha-1,4-glucosidase	1	6849	BTF1_27975	1	2013-07-16 13:39:41	2013-07-16 13:39:41
+6850	protein_coding	21	11	5461366	5463003	1	91184	ensembl		PTS system transporter subunit IICB	1	6850	BTF1_27980	1	2013-07-16 13:28:27	2013-07-16 13:28:27
+6851	protein_coding	21	11	5463008	5463799	1	91210	ensembl		exodeoxyribonuclease III	1	6851	BTF1_27985	1	2013-07-16 13:38:08	2013-07-16 13:38:08
+6852	protein_coding	21	11	5464105	5466966	1	91219	ensembl		phage infection protein	1	6852	BTF1_27990	1	2013-07-16 13:35:17	2013-07-16 13:35:17
+6853	protein_coding	21	11	5467007	5469196	-1	91230	ensembl		DNA topoisomerase III	1	6853	BTF1_27995	1	2013-07-16 13:14:36	2013-07-16 13:14:36
+6854	protein_coding	21	11	5469573	5470382	1	91257	ensembl		hydroxyethylthiazole kinase	1	6854	BTF1_28000	1	2013-07-16 13:16:51	2013-07-16 13:16:51
+6855	protein_coding	21	11	5470400	5471056	1	91277	ensembl		thiamine-phosphate pyrophosphorylase	1	6855	BTF1_28005	1	2013-07-16 13:28:09	2013-07-16 13:28:09
+6856	protein_coding	21	11	5471173	5472486	-1	91297	ensembl		anaerobic C4-dicarboxylate transporter	1	6856	BTF1_28010	1	2013-07-16 13:07:55	2013-07-16 13:07:55
+6857	protein_coding	21	11	5472987	5474729	1	91311	ensembl		methyl-accepting chemotaxis protein	1	6857	BTF1_28015	1	2013-07-16 13:11:53	2013-07-16 13:11:53
+6858	protein_coding	21	11	5474867	5478448	1	91329	ensembl		linear gramicidin synthetase subunit C	1	6858	BTF1_28020	1	2013-07-16 13:18:02	2013-07-16 13:18:02
+6859	protein_coding	21	11	5478704	5479024	1	91347	ensembl		hypothetical protein	1	6859	BTF1_28025	1	2013-07-16 13:13:54	2013-07-16 13:13:54
+6860	protein_coding	21	11	5478996	5479769	1	91358	ensembl		hydroxymethylpyrimidine transport system permease	1	6860	BTF1_28030	1	2013-07-16 13:42:57	2013-07-16 13:42:57
+6861	protein_coding	21	11	5479766	5480764	1	91373	ensembl		hydroxymethylpyrimidine-binding protein	1	6861	BTF1_28035	1	2013-07-16 13:19:08	2013-07-16 13:19:08
+6862	protein_coding	21	11	5480761	5481510	1	91386	ensembl		ABC transporter ATP-binding protein	1	6862	BTF1_28040	1	2013-07-16 13:32:58	2013-07-16 13:32:58
+6863	protein_coding	21	11	5481906	5483450	1	91405	ensembl		ABC transporter ATP-binding protein	1	6863	BTF1_28045	1	2013-07-16 13:32:53	2013-07-16 13:32:53
+6864	protein_coding	21	11	5483891	5485915	-1	91424	ensembl		chitinase B	1	6864	BTF1_28050	1	2013-07-16 13:41:04	2013-07-16 13:41:04
+6865	protein_coding	21	11	5486287	5486658	1	91450	ensembl		hypothetical protein	1	6865	BTF1_28055	1	2013-07-16 13:41:32	2013-07-16 13:41:32
+6866	protein_coding	21	11	5486669	5486983	1	91460	ensembl		hypothetical protein	1	6866	BTF1_28060	1	2013-07-16 13:11:32	2013-07-16 13:11:32
+6867	protein_coding	21	11	5486997	5487239	1	91472	ensembl		hypothetical protein	1	6867	BTF1_28065	1	2013-07-16 13:14:08	2013-07-16 13:14:08
+6868	protein_coding	21	11	5487365	5487508	1	91480	ensembl		hypothetical protein	1	6868	BTF1_28070	1	2013-07-16 13:12:04	2013-07-16 13:12:04
+6869	protein_coding	21	11	5487589	5488170	1	91489	ensembl		TetR family transcriptional regulator	1	6869	BTF1_28075	1	2013-07-16 13:21:11	2013-07-16 13:21:11
+6870	protein_coding	21	11	5488237	5489469	1	91510	ensembl		major facilitator family transporter	1	6870	BTF1_28080	1	2013-07-16 13:11:12	2013-07-16 13:11:12
+6871	protein_coding	21	11	5489583	5489777	1	91522	ensembl		DNA-binding protein	1	6871	BTF1_28085	1	2013-07-16 13:12:54	2013-07-16 13:12:54
+6872	protein_coding	21	11	5489847	5491130	-1	91534	ensembl		hypothetical protein	1	6872	BTF1_28090	1	2013-07-16 13:32:05	2013-07-16 13:32:05
+6873	protein_coding	21	11	5491239	5492552	-1	91546	ensembl		type I phosphodiesterase/nucleotide pyrophosphatase	1	6873	BTF1_28095	1	2013-07-16 13:20:17	2013-07-16 13:20:17
+6874	protein_coding	21	11	5492706	5492999	1	91560	ensembl		hypothetical protein	1	6874	BTF1_28100	1	2013-07-16 13:38:57	2013-07-16 13:38:57
+6875	protein_coding	21	11	5493350	5494780	1	91570	ensembl		prolyl-tRNA ligase	1	6875	BTF1_28105	1	2013-07-16 13:36:29	2013-07-16 13:36:29
+6876	protein_coding	21	11	5494895	315	-1	91593	ensembl		lpxtg-motif cell wall anchor domain-containing protein	1	6876	BTF1_00005	1	2013-07-16 13:43:36	2013-07-16 13:43:36
+6877	protein_coding	21	11	529	1407	1	91603	ensembl		ROK family protein	1	6877	BTF1_00010	1	2013-07-16 13:36:41	2013-07-16 13:36:41
+6878	protein_coding	21	11	1536	2132	1	91613	ensembl		Tellurium resistance protein terD/terE/terZ family	1	6878	BTF1_00015	1	2013-07-16 13:09:10	2013-07-16 13:09:10
+6879	protein_coding	21	11	2156	2740	1	91625	ensembl		tellurium resistance protein	1	6879	BTF1_00020	1	2013-07-16 13:08:16	2013-07-16 13:08:16
+6880	protein_coding	21	11	2826	3404	1	91637	ensembl		tellurium resistance protein	1	6880	BTF1_00025	1	2013-07-16 13:18:54	2013-07-16 13:18:54
+6881	protein_coding	21	11	3477	4268	1	91649	ensembl		tellurium resistance protein	1	6881	BTF1_00030	1	2013-07-16 13:37:12	2013-07-16 13:37:12
+6882	protein_coding	21	11	4378	6009	1	91661	ensembl		hypothetical protein	1	6882	BTF1_00035	1	2013-07-16 13:31:30	2013-07-16 13:31:30
+6883	protein_coding	21	11	6028	7110	1	91670	ensembl		Tellurite resistance protein	1	6883	BTF1_00040	1	2013-07-16 13:19:21	2013-07-16 13:19:21
+6884	protein_coding	21	11	7146	9812	-1	91680	ensembl		cation-transporting ATPase	1	6884	BTF1_00045	1	2013-07-16 13:24:54	2013-07-16 13:24:54
diff --git a/modules/t/test-genome-DBs/circ/core/meta.txt b/modules/t/test-genome-DBs/circ/core/meta.txt
index c9c62bac4e..00ce8bde9b 100644
--- a/modules/t/test-genome-DBs/circ/core/meta.txt
+++ b/modules/t/test-genome-DBs/circ/core/meta.txt
@@ -94,3 +94,4 @@
 40	1	species.taxonomy_id	1217737
 31	1	species.url	Bacillus_thuringiensis
 55	1	transcriptbuild.level	toplevel
+97	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/circ/core/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index ebd656a1de..66cf625678 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -21,27 +21,27 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -151,7 +151,7 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,13 +236,13 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -297,14 +297,14 @@ CREATE TABLE `gene` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,9 +500,9 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
@@ -511,14 +511,14 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=81424 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `ontology_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -652,13 +652,13 @@ CREATE TABLE `protein_feature` (
   KEY `translation_id` (`translation_id`),
   KEY `hitname_index` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
@@ -686,18 +686,18 @@ CREATE TABLE `repeat_feature` (
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -725,22 +725,22 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=37 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -781,12 +781,12 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,18 +817,18 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,23 +854,23 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
   KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=91703 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
diff --git a/modules/t/test-genome-DBs/circ/core/transcript.txt b/modules/t/test-genome-DBs/circ/core/transcript.txt
index a89a49372c..bafc475059 100644
--- a/modules/t/test-genome-DBs/circ/core/transcript.txt
+++ b/modules/t/test-genome-DBs/circ/core/transcript.txt
@@ -1,259 +1,259 @@
-6626	6626	21	3	700	2754	-1	88461	ensembl	protein_coding	ANNOTATED	\N	1	6463	AFQ30217	1	2013-07-16 13:03:32	2013-07-16 13:03:32
-6627	6627	21	3	2758	4539	-1	88470	ensembl	protein_coding	ANNOTATED	\N	1	6464	AFQ30218	1	2013-07-16 13:03:51	2013-07-16 13:03:51
-6628	6628	21	3	4552	5766	-1	88478	ensembl	protein_coding	ANNOTATED	\N	1	6465	AFQ30219	1	2013-07-16 13:03:57	2013-07-16 13:03:57
-6629	6629	21	3	5781	6728	-1	88486	ensembl	protein_coding	ANNOTATED	\N	1	6466	AFQ30220	1	2013-07-16 13:03:17	2013-07-16 13:03:17
-6630	6630	21	3	6744	7493	-1	88494	ensembl	protein_coding	ANNOTATED	\N	1	6467	AFQ30221	1	2013-07-16 13:03:24	2013-07-16 13:03:24
-6631	6631	21	3	7496	7870	-1	88502	ensembl	protein_coding	ANNOTATED	\N	1	6468	AFQ30222	1	2013-07-16 13:03:25	2013-07-16 13:03:25
-6632	6632	21	3	7968	8195	-1	88510	ensembl	protein_coding	ANNOTATED	\N	1	6469	AFQ30223	1	2013-07-16 13:04:10	2013-07-16 13:04:10
-6633	6633	21	3	8271	8933	-1	88519	ensembl	protein_coding	ANNOTATED	\N	1	6470	AFQ30224	1	2013-07-16 13:04:09	2013-07-16 13:04:09
-6634	6634	21	3	230089	230622	1	88527	ensembl	protein_coding	ANNOTATED	\N	1	6471	AFQ30448	1	2013-07-16 13:03:54	2013-07-16 13:03:54
-6635	6635	21	3	230700	230885	1	88535	ensembl	protein_coding	ANNOTATED	\N	1	6472	AFQ30449	1	2013-07-16 13:03:16	2013-07-16 13:03:16
-6636	6636	21	3	230948	231418	1	88543	ensembl	protein_coding	ANNOTATED	\N	1	6473	AFQ30450	1	2013-07-16 13:03:37	2013-07-16 13:03:37
-6637	6637	21	3	231603	231902	1	88551	ensembl	protein_coding	ANNOTATED	\N	1	6474	AFQ30451	1	2013-07-16 13:04:15	2013-07-16 13:04:15
-6638	6638	21	3	232697	232912	1	88559	ensembl	protein_coding	ANNOTATED	\N	1	6475	AFQ30452	1	2013-07-16 13:03:31	2013-07-16 13:03:31
-6639	6639	21	3	232927	233595	-1	88567	ensembl	protein_coding	ANNOTATED	\N	1	6476	AFQ30453	1	2013-07-16 13:04:11	2013-07-16 13:04:11
-6640	6640	21	3	233785	233991	1	88575	ensembl	protein_coding	ANNOTATED	\N	1	6477	AFQ30454	1	2013-07-16 13:03:49	2013-07-16 13:03:49
-6641	6641	21	3	234076	235323	-1	88583	ensembl	protein_coding	ANNOTATED	\N	1	6478	AFQ30455	1	2013-07-16 13:03:34	2013-07-16 13:03:34
-6642	6642	21	3	235337	685	-1	88591	ensembl	protein_coding	ANNOTATED	\N	1	6479	AFQ30216	1	2013-07-16 13:03:58	2013-07-16 13:03:58
-6643	6643	21	3	150202	151044	1	88607	ensembl	protein_coding	ANNOTATED	\N	1	6480	AFQ30343	1	2013-07-16 13:03:44	2013-07-16 13:03:44
-6644	6644	21	3	151325	153892	1	88615	ensembl	protein_coding	ANNOTATED	\N	1	6481	AFQ30344	1	2013-07-16 13:04:07	2013-07-16 13:04:07
-6645	6645	21	3	153966	154949	1	88630	ensembl	protein_coding	ANNOTATED	\N	1	6482	AFQ30345	1	2013-07-16 13:04:11	2013-07-16 13:04:11
-6646	6646	28	3	155169	155243	1	88632	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31789	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6647	6647	28	3	155250	155329	1	88635	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31791	1	2013-07-16 13:04:16	2013-07-16 13:04:16
-6648	6648	28	3	155338	155425	1	88638	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31793	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6649	6649	28	3	155623	155697	1	88641	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31795	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6650	6650	28	3	155704	155775	1	88644	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31797	1	2013-07-16 13:04:18	2013-07-16 13:04:18
-6651	6651	28	3	155782	155854	1	88647	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31799	1	2013-07-16 13:04:18	2013-07-16 13:04:18
-6652	6652	28	3	156057	156133	1	88650	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31801	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6653	6653	28	3	156290	156363	1	88653	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31803	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6654	6654	28	3	156374	156448	1	88656	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31805	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6655	6655	28	3	156548	156621	1	88659	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31807	1	2013-07-16 13:04:16	2013-07-16 13:04:16
-6656	6656	28	3	156632	156705	1	88662	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31809	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6657	6657	28	3	156735	156807	1	88665	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31811	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6658	6658	21	3	156856	157386	1	88674	ensembl	protein_coding	ANNOTATED	\N	1	6483	AFQ30346	1	2013-07-16 13:03:59	2013-07-16 13:03:59
-6659	6659	28	3	157418	157494	1	88676	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31813	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6660	6660	28	3	157503	157575	1	88679	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31815	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6661	6661	28	3	157852	157935	1	88682	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31817	1	2013-07-16 13:04:17	2013-07-16 13:04:17
-6662	6662	28	3	157939	158012	1	88685	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31819	1	2013-07-16 13:04:18	2013-07-16 13:04:18
-6663	6663	28	3	158104	158192	1	88688	ensembl	tRNA	ANNOTATED	\N	1	\N	BTF1_t31821	1	2013-07-16 13:04:16	2013-07-16 13:04:16
-6664	6664	21	3	158412	158852	1	88697	ensembl	protein_coding	ANNOTATED	\N	1	6484	AFQ30347	1	2013-07-16 13:04:12	2013-07-16 13:04:12
-6665	6665	21	3	158878	159462	1	88715	ensembl	protein_coding	ANNOTATED	\N	1	6485	AFQ30348	1	2013-07-16 13:03:39	2013-07-16 13:03:39
-6666	6666	21	3	159476	159976	1	88723	ensembl	protein_coding	ANNOTATED	\N	1	6486	AFQ30349	1	2013-07-16 13:03:17	2013-07-16 13:03:17
-6667	6667	21	3	159997	160533	1	88739	ensembl	protein_coding	ANNOTATED	\N	1	6487	AFQ30350	1	2013-07-16 13:03:43	2013-07-16 13:03:43
-6668	6668	21	4	210132	210989	1	88747	ensembl	protein_coding	ANNOTATED	\N	1	6488	AFQ30645	1	2013-07-16 13:04:34	2013-07-16 13:04:34
-6669	6669	21	4	211116	212180	1	88755	ensembl	protein_coding	ANNOTATED	\N	1	6489	AFQ30646	1	2013-07-16 13:04:43	2013-07-16 13:04:43
-6670	6670	21	4	212807	213178	1	88763	ensembl	protein_coding	ANNOTATED	\N	1	6490	AFQ30647	1	2013-07-16 13:04:52	2013-07-16 13:04:52
-6671	6671	21	4	213615	213926	1	88772	ensembl	protein_coding	ANNOTATED	\N	1	6491	AFQ30648	1	2013-07-16 13:04:34	2013-07-16 13:04:34
-6672	6672	21	4	213957	214370	1	88786	ensembl	protein_coding	ANNOTATED	\N	1	6492	AFQ30649	1	2013-07-16 13:05:04	2013-07-16 13:05:04
-6673	6673	21	4	215358	215726	1	88795	ensembl	protein_coding	ANNOTATED	\N	1	6493	AFQ30650	1	2013-07-16 13:04:44	2013-07-16 13:04:44
-6674	6674	21	4	215708	216049	1	88803	ensembl	protein_coding	ANNOTATED	\N	1	6494	AFQ30651	1	2013-07-16 13:04:33	2013-07-16 13:04:33
-6675	6675	21	4	216280	217335	1	88812	ensembl	protein_coding	ANNOTATED	\N	1	6495	AFQ30652	1	2013-07-16 13:05:02	2013-07-16 13:05:02
-6676	6676	21	4	217755	218327	1	88820	ensembl	protein_coding	ANNOTATED	\N	1	6496	AFQ30653	1	2013-07-16 13:05:03	2013-07-16 13:05:03
-6677	6677	21	4	218689	219771	1	88835	ensembl	protein_coding	ANNOTATED	\N	1	6497	AFQ30654	1	2013-07-16 13:05:05	2013-07-16 13:05:05
-6678	6678	21	4	220171	220830	-1	88850	ensembl	protein_coding	ANNOTATED	\N	1	6498	AFQ30655	1	2013-07-16 13:04:36	2013-07-16 13:04:36
-6679	6679	21	4	221204	221416	1	88858	ensembl	protein_coding	ANNOTATED	\N	1	6499	AFQ30656	1	2013-07-16 13:04:24	2013-07-16 13:04:24
-6680	6680	21	4	221988	222215	1	88876	ensembl	protein_coding	ANNOTATED	\N	1	6500	AFQ30657	1	2013-07-16 13:04:46	2013-07-16 13:04:46
-6681	6681	21	4	222287	432	1	88891	ensembl	protein_coding	ANNOTATED	\N	1	6501	AFQ30658	1	2013-07-16 13:04:21	2013-07-16 13:04:21
-6682	6682	21	4	572	1483	-1	88901	ensembl	protein_coding	ANNOTATED	\N	1	6502	AFQ30456	1	2013-07-16 13:04:22	2013-07-16 13:04:22
-6683	6683	21	4	1640	2599	-1	88912	ensembl	protein_coding	ANNOTATED	\N	1	6503	AFQ30457	1	2013-07-16 13:04:31	2013-07-16 13:04:31
-6684	6684	21	4	2873	3121	1	88920	ensembl	protein_coding	ANNOTATED	\N	1	6504	AFQ30458	1	2013-07-16 13:04:43	2013-07-16 13:04:43
-6685	6685	21	4	3135	3731	1	88935	ensembl	protein_coding	ANNOTATED	\N	1	6505	AFQ30459	1	2013-07-16 13:04:43	2013-07-16 13:04:43
-6686	6686	21	4	3847	4158	-1	88944	ensembl	protein_coding	ANNOTATED	\N	1	6506	AFQ30460	1	2013-07-16 13:05:02	2013-07-16 13:05:02
-6687	6687	21	4	4626	5060	-1	88952	ensembl	protein_coding	ANNOTATED	\N	1	6507	AFQ30461	1	2013-07-16 13:04:38	2013-07-16 13:04:38
-6688	6688	21	4	5444	6019	-1	88960	ensembl	protein_coding	ANNOTATED	\N	1	6508	AFQ30462	1	2013-07-16 13:04:53	2013-07-16 13:04:53
-6689	6689	21	4	7087	8286	-1	88976	ensembl	protein_coding	ANNOTATED	\N	1	6509	AFQ30463	1	2013-07-16 13:04:41	2013-07-16 13:04:41
-6690	6690	21	4	8316	8516	-1	88984	ensembl	protein_coding	ANNOTATED	\N	1	6510	AFQ30464	1	2013-07-16 13:05:05	2013-07-16 13:05:05
-6691	6691	21	4	8683	8943	-1	88992	ensembl	protein_coding	ANNOTATED	\N	1	6511	AFQ30465	1	2013-07-16 13:05:01	2013-07-16 13:05:01
-6692	6692	21	4	9011	10948	-1	89000	ensembl	protein_coding	ANNOTATED	\N	1	6512	AFQ30466	1	2013-07-16 13:04:45	2013-07-16 13:04:45
-6693	6693	21	7	347058	347492	-1	89008	ensembl	protein_coding	ANNOTATED	\N	1	6513	AFQ30213	1	2013-07-16 13:05:41	2013-07-16 13:05:41
-6694	6694	21	7	347641	348741	-1	89016	ensembl	protein_coding	ANNOTATED	\N	1	6514	AFQ30214	1	2013-07-16 13:06:06	2013-07-16 13:06:06
-6695	6695	21	7	348754	349407	-1	89024	ensembl	protein_coding	ANNOTATED	\N	1	6515	AFQ30215	1	2013-07-16 13:06:29	2013-07-16 13:06:29
-6696	6696	21	7	349459	333	-1	89032	ensembl	protein_coding	ANNOTATED	\N	1	6516	AFQ29782	1	2013-07-16 13:06:14	2013-07-16 13:06:14
-6697	6697	21	7	453	1598	-1	89040	ensembl	protein_coding	ANNOTATED	\N	1	6517	AFQ29783	1	2013-07-16 13:06:04	2013-07-16 13:06:04
-6698	6698	21	7	1612	1947	-1	89048	ensembl	protein_coding	ANNOTATED	\N	1	6518	AFQ29784	1	2013-07-16 13:05:49	2013-07-16 13:05:49
-6699	6699	21	7	2425	2937	-1	89056	ensembl	protein_coding	ANNOTATED	\N	1	6519	AFQ29785	1	2013-07-16 13:05:26	2013-07-16 13:05:26
-6700	6700	21	7	2957	3427	-1	89064	ensembl	protein_coding	ANNOTATED	\N	1	6520	AFQ29786	1	2013-07-16 13:05:35	2013-07-16 13:05:35
-6701	6701	21	7	3458	3892	-1	89072	ensembl	protein_coding	ANNOTATED	\N	1	6521	AFQ29787	1	2013-07-16 13:05:15	2013-07-16 13:05:15
-6702	6702	21	7	4042	4494	-1	89080	ensembl	protein_coding	ANNOTATED	\N	1	6522	AFQ29788	1	2013-07-16 13:05:33	2013-07-16 13:05:33
-6703	6703	21	7	4528	4965	-1	89088	ensembl	protein_coding	ANNOTATED	\N	1	6523	AFQ29789	1	2013-07-16 13:05:38	2013-07-16 13:05:38
-6704	6704	21	11	5300113	5300397	1	89096	ensembl	protein_coding	ANNOTATED	\N	1	6524	AFQ29625	1	2013-07-16 13:09:18	2013-07-16 13:09:18
-6705	6705	21	11	5300922	5301548	1	89104	ensembl	protein_coding	ANNOTATED	\N	1	6525	AFQ29626	1	2013-07-16 13:31:48	2013-07-16 13:31:48
-6706	6706	21	11	5301578	5302180	1	89118	ensembl	protein_coding	ANNOTATED	\N	1	6526	AFQ29627	1	2013-07-16 13:25:20	2013-07-16 13:25:20
-6707	6707	21	11	5302408	5303115	1	89126	ensembl	protein_coding	ANNOTATED	\N	1	6527	AFQ29628	1	2013-07-16 13:12:50	2013-07-16 13:12:50
-6708	6708	21	11	5303151	5304335	1	89140	ensembl	protein_coding	ANNOTATED	\N	1	6528	AFQ29629	1	2013-07-16 13:15:34	2013-07-16 13:15:34
-6709	6709	21	11	5304508	5305038	-1	89149	ensembl	protein_coding	ANNOTATED	\N	1	6529	AFQ29630	1	2013-07-16 13:36:54	2013-07-16 13:36:54
-6710	6710	21	11	5305053	5306660	-1	89163	ensembl	protein_coding	ANNOTATED	\N	1	6530	AFQ29631	1	2013-07-16 13:29:49	2013-07-16 13:29:49
-6711	6711	21	11	5306860	5307246	1	89172	ensembl	protein_coding	ANNOTATED	\N	1	6531	AFQ29632	1	2013-07-16 13:24:02	2013-07-16 13:24:02
-6712	6712	21	11	5308066	5309604	1	89202	ensembl	protein_coding	ANNOTATED	\N	1	6532	AFQ29633	1	2013-07-16 13:09:04	2013-07-16 13:09:04
-6713	6713	21	11	5309909	5310424	1	89210	ensembl	protein_coding	ANNOTATED	\N	1	6533	AFQ29634	1	2013-07-16 13:30:56	2013-07-16 13:30:56
-6714	6714	21	11	5310421	5311137	1	89218	ensembl	protein_coding	ANNOTATED	\N	1	6534	AFQ29635	1	2013-07-16 13:26:15	2013-07-16 13:26:15
-6715	6715	21	11	5311140	5312159	1	89226	ensembl	protein_coding	ANNOTATED	\N	1	6535	AFQ29636	1	2013-07-16 13:07:13	2013-07-16 13:07:13
-6716	6716	21	11	5312477	5312884	1	89234	ensembl	protein_coding	ANNOTATED	\N	1	6536	AFQ29637	1	2013-07-16 13:40:17	2013-07-16 13:40:17
-6717	6717	21	11	5313273	5313545	1	89242	ensembl	protein_coding	ANNOTATED	\N	1	6537	AFQ29638	1	2013-07-16 13:37:40	2013-07-16 13:37:40
-6718	6718	21	11	5313814	5315220	1	89265	ensembl	protein_coding	ANNOTATED	\N	1	6538	AFQ29639	1	2013-07-16 13:39:16	2013-07-16 13:39:16
-6719	6719	21	11	5315514	5316017	1	89273	ensembl	protein_coding	ANNOTATED	\N	1	6539	AFQ29640	1	2013-07-16 13:14:28	2013-07-16 13:14:28
-6720	6720	21	11	5315998	5317026	1	89289	ensembl	protein_coding	ANNOTATED	\N	1	6540	AFQ29641	1	2013-07-16 13:08:35	2013-07-16 13:08:35
-6721	6721	21	11	5317047	5317253	1	89298	ensembl	protein_coding	ANNOTATED	\N	1	6541	AFQ29642	1	2013-07-16 13:38:43	2013-07-16 13:38:43
-6722	6722	21	11	5317250	5318503	1	89317	ensembl	protein_coding	ANNOTATED	\N	1	6542	AFQ29643	1	2013-07-16 13:29:35	2013-07-16 13:29:35
-6723	6723	21	11	5318504	5319310	1	89330	ensembl	protein_coding	ANNOTATED	\N	1	6543	AFQ29644	1	2013-07-16 13:09:02	2013-07-16 13:09:02
-6724	6724	21	11	5319297	5319689	1	89338	ensembl	protein_coding	ANNOTATED	\N	1	6544	AFQ29645	1	2013-07-16 13:42:07	2013-07-16 13:42:07
-6725	6725	21	11	5320179	5321504	1	89355	ensembl	protein_coding	ANNOTATED	\N	1	6545	AFQ29646	1	2013-07-16 13:12:33	2013-07-16 13:12:33
-6726	6726	21	11	5321798	5322499	1	89376	ensembl	protein_coding	ANNOTATED	\N	1	6546	AFQ29647	1	2013-07-16 13:43:11	2013-07-16 13:43:11
-6727	6727	21	11	5322483	5323988	1	89399	ensembl	protein_coding	ANNOTATED	\N	1	6547	AFQ29648	1	2013-07-16 13:23:41	2013-07-16 13:23:41
-6728	6728	28	11	5324281	5325843	1	89401	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28371	1	2013-07-16 13:44:01	2013-07-16 13:44:01
-6729	6729	28	11	5325982	5328906	1	89404	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28399	1	2013-07-16 13:43:58	2013-07-16 13:43:58
-6730	6730	28	11	5328953	5329068	1	89407	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28343	1	2013-07-16 13:44:00	2013-07-16 13:44:00
-6731	6731	21	11	5329301	5330260	1	89420	ensembl	protein_coding	ANNOTATED	\N	1	6548	AFQ29649	1	2013-07-16 13:36:53	2013-07-16 13:36:53
-6732	6732	21	11	5330461	5331192	1	89433	ensembl	protein_coding	ANNOTATED	\N	1	6549	AFQ29650	1	2013-07-16 13:38:09	2013-07-16 13:38:09
-6733	6733	28	11	5331540	5333102	1	89435	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28373	1	2013-07-16 13:43:54	2013-07-16 13:43:54
-6734	6734	28	11	5333241	5336165	1	89438	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28401	1	2013-07-16 13:43:54	2013-07-16 13:43:54
-6735	6735	28	11	5336211	5336326	1	89441	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28345	1	2013-07-16 13:43:59	2013-07-16 13:43:59
-6736	6736	21	11	5336495	5336923	-1	89459	ensembl	protein_coding	ANNOTATED	\N	1	6550	AFQ29651	1	2013-07-16 13:15:40	2013-07-16 13:15:40
-6737	6737	28	11	5339054	5340616	1	89461	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28375	1	2013-07-16 13:43:55	2013-07-16 13:43:55
-6738	6738	28	11	5340755	5343679	1	89464	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28403	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6739	6739	28	11	5343725	5343840	1	89467	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28347	1	2013-07-16 13:43:57	2013-07-16 13:43:57
-6740	6740	21	11	5343916	5344374	-1	89479	ensembl	protein_coding	ANNOTATED	\N	1	6551	AFQ29652	1	2013-07-16 13:15:03	2013-07-16 13:15:03
-6741	6741	21	11	5344731	5345528	-1	89503	ensembl	protein_coding	ANNOTATED	\N	1	6552	AFQ29653	1	2013-07-16 13:29:26	2013-07-16 13:29:26
-6742	6742	21	11	5345546	5346283	-1	89511	ensembl	protein_coding	ANNOTATED	\N	1	6553	AFQ29654	1	2013-07-16 13:34:14	2013-07-16 13:34:14
-6743	6743	21	11	5346276	5347205	-1	89530	ensembl	protein_coding	ANNOTATED	\N	1	6554	AFQ29655	1	2013-07-16 13:27:09	2013-07-16 13:27:09
-6744	6744	21	11	5347274	5348287	-1	89554	ensembl	protein_coding	ANNOTATED	\N	1	6555	AFQ29656	1	2013-07-16 13:20:05	2013-07-16 13:20:05
-6745	6745	21	11	5348277	5348990	-1	89575	ensembl	protein_coding	ANNOTATED	\N	1	6556	AFQ29657	1	2013-07-16 13:33:30	2013-07-16 13:33:30
-6746	6746	28	11	5349468	5351030	1	89577	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28377	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6747	6747	28	11	5351169	5354093	1	89580	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28405	1	2013-07-16 13:43:54	2013-07-16 13:43:54
-6748	6748	28	11	5354139	5354254	1	89583	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28349	1	2013-07-16 13:43:58	2013-07-16 13:43:58
-6749	6749	21	11	5354467	5355387	1	89596	ensembl	protein_coding	ANNOTATED	\N	1	6557	AFQ29658	1	2013-07-16 13:23:57	2013-07-16 13:23:57
-6750	6750	21	11	5355474	5356265	-1	89610	ensembl	protein_coding	ANNOTATED	\N	1	6558	AFQ29659	1	2013-07-16 13:21:59	2013-07-16 13:21:59
-6751	6751	28	11	5356579	5358141	1	89612	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28379	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6752	6752	28	11	5358280	5361204	1	89615	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28407	1	2013-07-16 13:43:53	2013-07-16 13:43:53
-6753	6753	28	11	5361251	5361366	1	89618	ensembl	rRNA	ANNOTATED	\N	1	\N	BTF1_r28351	1	2013-07-16 13:43:55	2013-07-16 13:43:55
-6754	6754	21	11	5362106	5362591	1	89634	ensembl	protein_coding	ANNOTATED	\N	1	6559	AFQ29660	1	2013-07-16 13:12:36	2013-07-16 13:12:36
-6755	6755	21	11	5362588	5363739	1	89663	ensembl	protein_coding	ANNOTATED	\N	1	6560	AFQ29661	1	2013-07-16 13:07:35	2013-07-16 13:07:35
-6756	6756	21	11	5363736	5365043	1	89686	ensembl	protein_coding	ANNOTATED	\N	1	6561	AFQ29662	1	2013-07-16 13:17:58	2013-07-16 13:17:58
-6757	6757	21	11	5365132	5365851	1	89704	ensembl	protein_coding	ANNOTATED	\N	1	6562	AFQ29663	1	2013-07-16 13:14:58	2013-07-16 13:14:58
-6758	6758	21	11	5365844	5366098	1	89716	ensembl	protein_coding	ANNOTATED	\N	1	6563	AFQ29664	1	2013-07-16 13:12:48	2013-07-16 13:12:48
-6759	6759	21	11	5366095	5366778	1	89737	ensembl	protein_coding	ANNOTATED	\N	1	6564	AFQ29665	1	2013-07-16 13:20:46	2013-07-16 13:20:46
-6760	6760	21	11	5366762	5368981	1	89758	ensembl	protein_coding	ANNOTATED	\N	1	6565	AFQ29666	1	2013-07-16 13:29:17	2013-07-16 13:29:17
-6761	6761	21	11	5368966	5370381	1	89781	ensembl	protein_coding	ANNOTATED	\N	1	6566	AFQ29667	1	2013-07-16 13:10:58	2013-07-16 13:10:58
-6762	6762	21	11	5370487	5371527	1	89802	ensembl	protein_coding	ANNOTATED	\N	1	6567	AFQ29668	1	2013-07-16 13:36:20	2013-07-16 13:36:20
-6763	6763	21	11	5371524	5372111	1	89822	ensembl	protein_coding	ANNOTATED	\N	1	6568	AFQ29669	1	2013-07-16 13:23:37	2013-07-16 13:23:37
-6764	6764	21	11	5372136	5373671	1	89841	ensembl	protein_coding	ANNOTATED	\N	1	6569	AFQ29670	1	2013-07-16 13:40:41	2013-07-16 13:40:41
-6765	6765	21	11	5374051	5375322	1	89872	ensembl	protein_coding	ANNOTATED	\N	1	6570	AFQ29671	1	2013-07-16 13:22:35	2013-07-16 13:22:35
-6766	6766	21	11	5375359	5375523	-1	89886	ensembl	protein_coding	ANNOTATED	\N	1	6571	AFQ29672	1	2013-07-16 13:41:32	2013-07-16 13:41:32
-6767	6767	21	11	5375539	5376384	-1	89899	ensembl	protein_coding	ANNOTATED	\N	1	6572	AFQ29673	1	2013-07-16 13:27:17	2013-07-16 13:27:17
-6768	6768	21	11	5376603	5376980	-1	89908	ensembl	protein_coding	ANNOTATED	\N	1	6573	AFQ29674	1	2013-07-16 13:42:21	2013-07-16 13:42:21
-6769	6769	21	11	5377262	5377951	1	89924	ensembl	protein_coding	ANNOTATED	\N	1	6574	AFQ29675	1	2013-07-16 13:41:32	2013-07-16 13:41:32
-6770	6770	21	11	5377952	5380213	1	89949	ensembl	protein_coding	ANNOTATED	\N	1	6575	AFQ29676	1	2013-07-16 13:30:44	2013-07-16 13:30:44
-6771	6771	21	11	5380228	5382237	1	89978	ensembl	protein_coding	ANNOTATED	\N	1	6576	AFQ29677	1	2013-07-16 13:16:58	2013-07-16 13:16:58
-6772	6772	21	11	5382254	5383447	1	89987	ensembl	protein_coding	ANNOTATED	\N	1	6577	AFQ29678	1	2013-07-16 13:26:19	2013-07-16 13:26:19
-6773	6773	21	11	5383544	5384314	1	89999	ensembl	protein_coding	ANNOTATED	\N	1	6578	AFQ29679	1	2013-07-16 13:34:50	2013-07-16 13:34:50
-6774	6774	21	11	5384468	5386015	1	90024	ensembl	protein_coding	ANNOTATED	\N	1	6579	AFQ29680	1	2013-07-16 13:22:13	2013-07-16 13:22:13
-6775	6775	21	11	5386286	5386831	-1	90036	ensembl	protein_coding	ANNOTATED	\N	1	6580	AFQ29681	1	2013-07-16 13:38:42	2013-07-16 13:38:42
-6776	6776	21	11	5387304	5388323	1	90062	ensembl	protein_coding	ANNOTATED	\N	1	6581	AFQ29682	1	2013-07-16 13:25:57	2013-07-16 13:25:57
-6777	6777	21	11	5388313	5388978	1	90078	ensembl	protein_coding	ANNOTATED	\N	1	6582	AFQ29683	1	2013-07-16 13:08:07	2013-07-16 13:08:07
-6778	6778	21	11	5389000	5389854	1	90087	ensembl	protein_coding	ANNOTATED	\N	1	6583	AFQ29684	1	2013-07-16 13:22:04	2013-07-16 13:22:04
-6779	6779	21	11	5390022	5390492	-1	90096	ensembl	protein_coding	ANNOTATED	\N	1	6584	AFQ29685	1	2013-07-16 13:25:05	2013-07-16 13:25:05
-6780	6780	21	11	5390551	5390742	-1	90105	ensembl	protein_coding	ANNOTATED	\N	1	6585	AFQ29686	1	2013-07-16 13:06:45	2013-07-16 13:06:45
-6781	6781	21	11	5390735	5391913	-1	90123	ensembl	protein_coding	ANNOTATED	\N	1	6586	AFQ29687	1	2013-07-16 13:27:19	2013-07-16 13:27:19
-6782	6782	21	11	5391992	5392474	-1	90142	ensembl	protein_coding	ANNOTATED	\N	1	6587	AFQ29688	1	2013-07-16 13:07:33	2013-07-16 13:07:33
-6783	6783	21	11	5392706	5392942	1	90151	ensembl	protein_coding	ANNOTATED	\N	1	6588	AFQ29689	1	2013-07-16 13:23:54	2013-07-16 13:23:54
-6784	6784	21	11	5393084	5393374	1	90171	ensembl	protein_coding	ANNOTATED	\N	1	6589	AFQ29690	1	2013-07-16 13:30:18	2013-07-16 13:30:18
-6785	6785	21	11	5393390	5394847	1	90192	ensembl	protein_coding	ANNOTATED	\N	1	6590	AFQ29691	1	2013-07-16 13:37:11	2013-07-16 13:37:11
-6786	6786	21	11	5394862	5396289	1	90215	ensembl	protein_coding	ANNOTATED	\N	1	6591	AFQ29692	1	2013-07-16 13:41:02	2013-07-16 13:41:02
-6787	6787	21	11	5396850	5397755	1	90233	ensembl	protein_coding	ANNOTATED	\N	1	6592	AFQ29693	1	2013-07-16 13:28:06	2013-07-16 13:28:06
-6788	6788	21	11	5397896	5398642	1	90246	ensembl	protein_coding	ANNOTATED	\N	1	6593	AFQ29694	1	2013-07-16 13:22:11	2013-07-16 13:22:11
-6789	6789	21	11	5398797	5400161	1	90266	ensembl	protein_coding	ANNOTATED	\N	1	6594	AFQ29695	1	2013-07-16 13:20:01	2013-07-16 13:20:01
-6790	6790	21	11	5400277	5401644	1	90298	ensembl	protein_coding	ANNOTATED	\N	1	6595	AFQ29696	1	2013-07-16 13:22:46	2013-07-16 13:22:46
-6791	6791	21	11	5401637	5403088	1	90317	ensembl	protein_coding	ANNOTATED	\N	1	6596	AFQ29697	1	2013-07-16 13:14:19	2013-07-16 13:14:19
-6792	6792	21	11	5403136	5403459	1	90333	ensembl	protein_coding	ANNOTATED	\N	1	6597	AFQ29698	1	2013-07-16 13:39:21	2013-07-16 13:39:21
-6793	6793	21	11	5403592	5404083	1	90345	ensembl	protein_coding	ANNOTATED	\N	1	6598	AFQ29699	1	2013-07-16 13:09:08	2013-07-16 13:09:08
-6794	6794	21	11	5404128	5405357	-1	90359	ensembl	protein_coding	ANNOTATED	\N	1	6599	AFQ29700	1	2013-07-16 13:26:05	2013-07-16 13:26:05
-6795	6795	21	11	5405474	5406556	-1	90375	ensembl	protein_coding	ANNOTATED	\N	1	6600	AFQ29701	1	2013-07-16 13:41:01	2013-07-16 13:41:01
-6796	6796	21	11	5406704	5406877	-1	90383	ensembl	protein_coding	ANNOTATED	\N	1	6601	AFQ29702	1	2013-07-16 13:35:08	2013-07-16 13:35:08
-6797	6797	21	11	5407094	5407801	1	90391	ensembl	protein_coding	ANNOTATED	\N	1	6602	AFQ29703	1	2013-07-16 13:20:00	2013-07-16 13:20:00
-6798	6798	21	11	5407848	5409044	-1	90410	ensembl	protein_coding	ANNOTATED	\N	1	6603	AFQ29704	1	2013-07-16 13:41:35	2013-07-16 13:41:35
-6799	6799	21	11	5409470	5410846	1	90432	ensembl	protein_coding	ANNOTATED	\N	1	6604	AFQ29705	1	2013-07-16 13:36:03	2013-07-16 13:36:03
-6800	6800	21	11	5411007	5411996	1	90451	ensembl	protein_coding	ANNOTATED	\N	1	6605	AFQ29706	1	2013-07-16 13:34:39	2013-07-16 13:34:39
-6801	6801	21	11	5412348	5412866	1	90460	ensembl	protein_coding	ANNOTATED	\N	1	6606	AFQ29707	1	2013-07-16 13:08:22	2013-07-16 13:08:22
-6802	6802	21	11	5412961	5413668	1	90474	ensembl	protein_coding	ANNOTATED	\N	1	6607	AFQ29708	1	2013-07-16 13:35:51	2013-07-16 13:35:51
-6803	6803	21	11	5413665	5413856	-1	90482	ensembl	protein_coding	ANNOTATED	\N	1	6608	AFQ29709	1	2013-07-16 13:22:27	2013-07-16 13:22:27
-6804	6804	21	11	5413888	5414583	-1	90495	ensembl	protein_coding	ANNOTATED	\N	1	6609	AFQ29710	1	2013-07-16 13:24:02	2013-07-16 13:24:02
-6805	6805	21	11	5414598	5415707	-1	90509	ensembl	protein_coding	ANNOTATED	\N	1	6610	AFQ29711	1	2013-07-16 13:25:27	2013-07-16 13:25:27
-6806	6806	21	11	5415801	5417072	1	90517	ensembl	protein_coding	ANNOTATED	\N	1	6611	AFQ29712	1	2013-07-16 13:35:40	2013-07-16 13:35:40
-6807	6807	21	11	5417061	5418482	-1	90532	ensembl	protein_coding	ANNOTATED	\N	1	6612	AFQ29713	1	2013-07-16 13:42:40	2013-07-16 13:42:40
-6808	6808	21	11	5418775	5419890	1	90546	ensembl	protein_coding	ANNOTATED	\N	1	6613	AFQ29714	1	2013-07-16 13:36:58	2013-07-16 13:36:58
-6809	6809	21	11	5420084	5420689	1	90554	ensembl	protein_coding	ANNOTATED	\N	1	6614	AFQ29715	1	2013-07-16 13:38:34	2013-07-16 13:38:34
-6810	6810	21	11	5420722	5422248	-1	90585	ensembl	protein_coding	ANNOTATED	\N	1	6615	AFQ29716	1	2013-07-16 13:19:13	2013-07-16 13:19:13
-6811	6811	21	11	5422263	5422826	-1	90605	ensembl	protein_coding	ANNOTATED	\N	1	6616	AFQ29717	1	2013-07-16 13:18:31	2013-07-16 13:18:31
-6812	6812	21	11	5423418	5424647	1	90625	ensembl	protein_coding	ANNOTATED	\N	1	6617	AFQ29718	1	2013-07-16 13:25:47	2013-07-16 13:25:47
-6813	6813	21	11	5424657	5425703	1	90644	ensembl	protein_coding	ANNOTATED	\N	1	6618	AFQ29719	1	2013-07-16 13:21:46	2013-07-16 13:21:46
-6814	6814	21	11	5425757	5426398	1	90658	ensembl	protein_coding	ANNOTATED	\N	1	6619	AFQ29720	1	2013-07-16 13:37:42	2013-07-16 13:37:42
-6815	6815	21	11	5426463	5427347	-1	90674	ensembl	protein_coding	ANNOTATED	\N	1	6620	AFQ29721	1	2013-07-16 13:18:06	2013-07-16 13:18:06
-6816	6816	21	11	5427314	5427619	-1	90691	ensembl	protein_coding	ANNOTATED	\N	1	6621	AFQ29722	1	2013-07-16 13:17:04	2013-07-16 13:17:04
-6817	6817	21	11	5427729	5428736	-1	90708	ensembl	protein_coding	ANNOTATED	\N	1	6622	AFQ29723	1	2013-07-16 13:23:17	2013-07-16 13:23:17
-6818	6818	21	11	5428733	5429749	-1	90724	ensembl	protein_coding	ANNOTATED	\N	1	6623	AFQ29724	1	2013-07-16 13:36:45	2013-07-16 13:36:45
-6819	6819	21	11	5429822	5430739	-1	90735	ensembl	protein_coding	ANNOTATED	\N	1	6624	AFQ29725	1	2013-07-16 13:17:36	2013-07-16 13:17:36
-6820	6820	21	11	5431071	5432120	1	90754	ensembl	protein_coding	ANNOTATED	\N	1	6625	AFQ29726	1	2013-07-16 13:07:40	2013-07-16 13:07:40
-6821	6821	21	11	5432316	5432684	-1	90762	ensembl	protein_coding	ANNOTATED	\N	1	6626	AFQ29727	1	2013-07-16 13:06:47	2013-07-16 13:06:47
-6822	6822	21	11	5432871	5433110	1	90774	ensembl	protein_coding	ANNOTATED	\N	1	6627	AFQ29728	1	2013-07-16 13:27:31	2013-07-16 13:27:31
-6823	6823	21	11	5433235	5433348	1	90782	ensembl	protein_coding	ANNOTATED	\N	1	6628	AFQ29729	1	2013-07-16 13:33:42	2013-07-16 13:33:42
-6824	6824	21	11	5433345	5433869	1	90793	ensembl	protein_coding	ANNOTATED	\N	1	6629	AFQ29730	1	2013-07-16 13:41:20	2013-07-16 13:41:20
-6825	6825	21	11	5433890	5434339	1	90804	ensembl	protein_coding	ANNOTATED	\N	1	6630	AFQ29731	1	2013-07-16 13:07:14	2013-07-16 13:07:14
-6826	6826	21	11	5434402	5434509	1	90812	ensembl	protein_coding	ANNOTATED	\N	1	6631	AFQ29732	1	2013-07-16 13:21:58	2013-07-16 13:21:58
-6827	6827	21	11	5434502	5435170	1	90821	ensembl	protein_coding	ANNOTATED	\N	1	6632	AFQ29733	1	2013-07-16 13:17:03	2013-07-16 13:17:03
-6828	6828	21	11	5435410	5436675	1	90835	ensembl	protein_coding	ANNOTATED	\N	1	6633	AFQ29734	1	2013-07-16 13:28:54	2013-07-16 13:28:54
-6829	6829	21	11	5436813	5438039	1	90859	ensembl	protein_coding	ANNOTATED	\N	1	6634	AFQ29735	1	2013-07-16 13:25:02	2013-07-16 13:25:02
-6830	6830	21	11	5438269	5438649	1	90867	ensembl	protein_coding	ANNOTATED	\N	1	6635	AFQ29736	1	2013-07-16 13:13:32	2013-07-16 13:13:32
-6831	6831	21	11	5438784	5439416	-1	90876	ensembl	protein_coding	ANNOTATED	\N	1	6636	AFQ29737	1	2013-07-16 13:39:09	2013-07-16 13:39:09
-6832	6832	21	11	5439766	5440875	1	90885	ensembl	protein_coding	ANNOTATED	\N	1	6637	AFQ29738	1	2013-07-16 13:26:23	2013-07-16 13:26:23
-6833	6833	21	11	5440987	5441769	1	90894	ensembl	protein_coding	ANNOTATED	\N	1	6638	AFQ29739	1	2013-07-16 13:38:43	2013-07-16 13:38:43
-6834	6834	21	11	5441783	5443084	-1	90910	ensembl	protein_coding	ANNOTATED	\N	1	6639	AFQ29740	1	2013-07-16 13:38:35	2013-07-16 13:38:35
-6835	6835	21	11	5443231	5444757	-1	90930	ensembl	protein_coding	ANNOTATED	\N	1	6640	AFQ29741	1	2013-07-16 13:25:19	2013-07-16 13:25:19
-6836	6836	21	11	5445339	5446424	1	90942	ensembl	protein_coding	ANNOTATED	\N	1	6641	AFQ29742	1	2013-07-16 13:29:55	2013-07-16 13:29:55
-6837	6837	21	11	5446478	5447170	-1	90959	ensembl	protein_coding	ANNOTATED	\N	1	6642	AFQ29743	1	2013-07-16 13:27:59	2013-07-16 13:27:59
-6838	6838	21	11	5447281	5448075	-1	90975	ensembl	protein_coding	ANNOTATED	\N	1	6643	AFQ29744	1	2013-07-16 13:42:24	2013-07-16 13:42:24
-6839	6839	21	11	5448197	5448919	-1	90994	ensembl	protein_coding	ANNOTATED	\N	1	6644	AFQ29745	1	2013-07-16 13:17:09	2013-07-16 13:17:09
-6840	6840	21	11	5449130	5450422	1	91009	ensembl	protein_coding	ANNOTATED	\N	1	6645	AFQ29746	1	2013-07-16 13:23:58	2013-07-16 13:23:58
-6841	6841	21	11	5450569	5451018	1	91037	ensembl	protein_coding	ANNOTATED	\N	1	6646	AFQ29747	1	2013-07-16 13:21:31	2013-07-16 13:21:31
-6842	6842	21	11	5451287	5452519	1	91054	ensembl	protein_coding	ANNOTATED	\N	1	6647	AFQ29748	1	2013-07-16 13:12:42	2013-07-16 13:12:42
-6843	6843	21	11	5452550	5453548	1	91074	ensembl	protein_coding	ANNOTATED	\N	1	6648	AFQ29749	1	2013-07-16 13:40:34	2013-07-16 13:40:34
-6844	6844	21	11	5453648	5455063	1	91094	ensembl	protein_coding	ANNOTATED	\N	1	6649	AFQ29750	1	2013-07-16 13:29:37	2013-07-16 13:29:37
-6845	6845	21	11	5455101	5456063	1	91111	ensembl	protein_coding	ANNOTATED	\N	1	6650	AFQ29751	1	2013-07-16 13:15:57	2013-07-16 13:15:57
-6846	6846	21	11	5456265	5456954	1	91134	ensembl	protein_coding	ANNOTATED	\N	1	6651	AFQ29752	1	2013-07-16 13:43:30	2013-07-16 13:43:30
-6847	6847	21	11	5457111	5457794	1	91142	ensembl	protein_coding	ANNOTATED	\N	1	6652	AFQ29753	1	2013-07-16 13:24:27	2013-07-16 13:24:27
-6848	6848	21	11	5457918	5459252	-1	91160	ensembl	protein_coding	ANNOTATED	\N	1	6653	AFQ29754	1	2013-07-16 13:29:36	2013-07-16 13:29:36
-6849	6849	21	11	5459496	5461160	1	91181	ensembl	protein_coding	ANNOTATED	\N	1	6654	AFQ29755	1	2013-07-16 13:39:41	2013-07-16 13:39:41
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-6851	6851	21	11	5463008	5463799	1	91217	ensembl	protein_coding	ANNOTATED	\N	1	6656	AFQ29757	1	2013-07-16 13:38:08	2013-07-16 13:38:08
-6852	6852	21	11	5464105	5466966	1	91227	ensembl	protein_coding	ANNOTATED	\N	1	6657	AFQ29758	1	2013-07-16 13:35:17	2013-07-16 13:35:17
-6853	6853	21	11	5467007	5469196	-1	91254	ensembl	protein_coding	ANNOTATED	\N	1	6658	AFQ29759	1	2013-07-16 13:14:36	2013-07-16 13:14:36
-6854	6854	21	11	5469573	5470382	1	91274	ensembl	protein_coding	ANNOTATED	\N	1	6659	AFQ29760	1	2013-07-16 13:16:51	2013-07-16 13:16:51
-6855	6855	21	11	5470400	5471056	1	91294	ensembl	protein_coding	ANNOTATED	\N	1	6660	AFQ29761	1	2013-07-16 13:28:09	2013-07-16 13:28:09
-6856	6856	21	11	5471173	5472486	-1	91308	ensembl	protein_coding	ANNOTATED	\N	1	6661	AFQ29762	1	2013-07-16 13:07:55	2013-07-16 13:07:55
-6857	6857	21	11	5472987	5474729	1	91326	ensembl	protein_coding	ANNOTATED	\N	1	6662	AFQ29763	1	2013-07-16 13:11:53	2013-07-16 13:11:53
-6858	6858	21	11	5474867	5478448	1	91345	ensembl	protein_coding	ANNOTATED	\N	1	6663	AFQ29764	1	2013-07-16 13:18:02	2013-07-16 13:18:02
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+6871	6871	21	11	5489583	5489777	1	91532	ensembl	protein_coding		\N	1	6676	AFQ29777	1	2013-07-16 13:12:54	2013-07-16 13:12:54
+6872	6872	21	11	5489847	5491130	-1	91543	ensembl	protein_coding		\N	1	6677	AFQ29778	1	2013-07-16 13:32:05	2013-07-16 13:32:05
+6873	6873	21	11	5491239	5492552	-1	91558	ensembl	protein_coding		\N	1	6678	AFQ29779	1	2013-07-16 13:20:17	2013-07-16 13:20:17
+6874	6874	21	11	5492706	5492999	1	91567	ensembl	protein_coding		\N	1	6679	AFQ29780	1	2013-07-16 13:38:57	2013-07-16 13:38:57
+6875	6875	21	11	5493350	5494780	1	91591	ensembl	protein_coding		\N	1	6680	AFQ29781	1	2013-07-16 13:36:29	2013-07-16 13:36:29
+6876	6876	21	11	5494895	315	-1	91601	ensembl	protein_coding		\N	1	6681	AFQ24231	1	2013-07-16 13:43:36	2013-07-16 13:43:36
+6877	6877	21	11	529	1407	1	91610	ensembl	protein_coding		\N	1	6682	AFQ24232	1	2013-07-16 13:36:41	2013-07-16 13:36:41
+6878	6878	21	11	1536	2132	1	91622	ensembl	protein_coding		\N	1	6683	AFQ24233	1	2013-07-16 13:09:10	2013-07-16 13:09:10
+6879	6879	21	11	2156	2740	1	91634	ensembl	protein_coding		\N	1	6684	AFQ24234	1	2013-07-16 13:08:16	2013-07-16 13:08:16
+6880	6880	21	11	2826	3404	1	91646	ensembl	protein_coding		\N	1	6685	AFQ24235	1	2013-07-16 13:18:54	2013-07-16 13:18:54
+6881	6881	21	11	3477	4268	1	91659	ensembl	protein_coding		\N	1	6686	AFQ24236	1	2013-07-16 13:37:12	2013-07-16 13:37:12
+6882	6882	21	11	4378	6009	1	91668	ensembl	protein_coding		\N	1	6687	AFQ24237	1	2013-07-16 13:31:30	2013-07-16 13:31:30
+6883	6883	21	11	6028	7110	1	91677	ensembl	protein_coding		\N	1	6688	AFQ24238	1	2013-07-16 13:19:21	2013-07-16 13:19:21
+6884	6884	21	11	7146	9812	-1	91702	ensembl	protein_coding		\N	1	6689	AFQ24239	1	2013-07-16 13:24:54	2013-07-16 13:24:54
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
index 78eb1b6f9c..767c1bbb50 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:24 2015
+-- Created on Fri May  6 15:43:56 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float(8,2) NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL,
-  type varchar(30) NOT NULL,
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,11 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -303,14 +301,12 @@ CREATE TABLE external_db (
   description text
 );
 
-CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
-
 --
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -380,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -396,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -418,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -437,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -471,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -484,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -496,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -510,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -522,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -531,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -577,24 +573,24 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
@@ -605,7 +601,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -619,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -637,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -664,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -680,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -693,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -714,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision(8,2),
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -735,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -746,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -762,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -796,7 +792,7 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
 CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
@@ -806,12 +802,12 @@ CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -824,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -860,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -911,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -933,7 +929,7 @@ CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, a
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -944,8 +940,6 @@ CREATE TABLE unmapped_object (
   parent varchar(255)
 );
 
-CREATE UNIQUE INDEX unique_unmapped_obj_idx ON unmapped_object (ensembl_id, ensembl_object_type, identifier, unmapped_reason_id, parent, external_db_id);
-
 --
 -- Table: unmapped_reason
 --
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/exon.txt b/modules/t/test-genome-DBs/homo_sapiens/core/exon.txt
index 1f53304f83..e1b69ff2fc 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/exon.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/exon.txt
@@ -159,4 +159,4 @@
 162032	469283	31222465	31222583	1	1	0	1	1	ENSE00001109601	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 162033	965899	10060	10405	1	0	0	1	1	ENSE00001109603	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 162034	469290	1	6	1	0	0	1	1	ENSE00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
-162035	469290	5	9	1	0	0	1	1	ENSE00000111112	1	2014-12-11 14:00:00	2014-12-11 14:00:00
\ No newline at end of file
+162035	469290	5	9	1	0	0	1	1	ENSE00000111112	1	2014-12-11 14:00:00	2014-12-11 14:00:00
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/gene.txt b/modules/t/test-genome-DBs/homo_sapiens/core/gene.txt
index 3ee67e2394..502f91f37f 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/gene.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/gene.txt
@@ -18,4 +18,4 @@
 18273	protein_coding	1282	469283	31166507	31196939	1	97759	ensembl	KNOWN	MICROTUBULE-ASSOCIATED PROTEIN RP/EB FAMILY MEMBER 1 (APC-BINDING PROTEIN EB1). [Source:SWISSPROT;Acc:Q15691]	1	21738	ENSG00000101367	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 18274	protein_coding	1282	469283	31210077	31225346	1	0	ensembl	NOVEL	\N	1	21739	ENSG00000167097	1	2004-12-06 12:00:00	2004-12-06 12:00:00
 18275	protein_coding	1282	965899	10060	10405	1	0	ensembl	NOVEL	\N	1	21740	ENSG00000355555	1	2004-12-06 12:00:00	2004-12-06 12:00:00
-18276	protein_coding	1282	469290	1	150	1	\N	ensembl	NOVEL	weird	1	21741	ENSG00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
\ No newline at end of file
+18276	protein_coding	1282	469290	1	150	1	\N	ensembl	NOVEL	weird	1	21741	ENSG00000111111	1	2014-12-11 14:00:00	2014-12-11 14:00:00
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
index e2d521e9d6..46c541821a 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/meta.txt
@@ -73,3 +73,4 @@
 133	\N	patch	patch_83_84_b.sql|xref.version_default
 134	\N	patch	patch_83_84_c.sql|protein_feature_unique
 135	\N	patch	patch_83_84_d.sql|longer_synonym
+136	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index ebd656a1de..7a86d34792 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
   PRIMARY KEY (`alt_allele_id`),
   UNIQUE KEY `gene_idx` (`gene_id`),
   KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `alt_allele_attrib` (
   `alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,32 +16,32 @@ CREATE TABLE `alt_allele_attrib` (
 CREATE TABLE `alt_allele_group` (
   `alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=8409 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -73,7 +73,7 @@ CREATE TABLE `assembly_exception` (
   PRIMARY KEY (`assembly_exception_id`),
   KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
   KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `associated_group` (
   `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=20 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -144,17 +144,17 @@ CREATE TABLE `density_feature` (
   PRIMARY KEY (`density_feature_id`),
   KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
   KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `density_type` (
   `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -172,7 +172,7 @@ CREATE TABLE `ditag` (
   `tag_count` smallint(6) DEFAULT '1',
   `sequence` text,
   PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `ditag_feature` (
   `ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -191,11 +191,11 @@ CREATE TABLE `ditag_feature` (
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
   KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4828763 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -223,7 +223,7 @@ CREATE TABLE `dna_align_feature` (
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=29797140 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `exon` (
   `exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -236,13 +236,13 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=162036 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -297,14 +297,14 @@ CREATE TABLE `gene` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=18277 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,29 +376,29 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_set` (
   `mapping_set_id` int(10) unsigned NOT NULL,
@@ -411,15 +411,15 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
   `marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -432,14 +432,14 @@ CREATE TABLE `marker_feature` (
   PRIMARY KEY (`marker_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,12 +448,12 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=137 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -489,7 +489,7 @@ CREATE TABLE `misc_feature` (
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_feature_misc_set` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -500,25 +500,25 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=253685 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `ontology_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -538,14 +538,14 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `name_idx` (`display_label`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon_transcript` (
   `operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -557,14 +557,14 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
   KEY `operon_idx` (`operon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon_transcript_gene` (
   `operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -574,11 +574,11 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_exon` (
   `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -594,7 +594,7 @@ CREATE TABLE `prediction_exon` (
   PRIMARY KEY (`prediction_exon_id`),
   KEY `prediction_transcript_id` (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=192 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_transcript` (
   `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -603,11 +603,11 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=18084 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `protein_align_feature` (
   `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -631,7 +631,7 @@ CREATE TABLE `protein_align_feature` (
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=11554505 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `protein_feature` (
   `protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -652,20 +652,20 @@ CREATE TABLE `protein_feature` (
   KEY `translation_id` (`translation_id`),
   KEY `hitname_index` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=242847 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
   KEY `class` (`repeat_class`),
   KEY `consensus` (`repeat_consensus`(10)),
   KEY `type` (`repeat_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1018 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_feature` (
   `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,22 +682,22 @@ CREATE TABLE `repeat_feature` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `repeat_idx` (`repeat_consensus_id`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=922515 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -717,7 +717,7 @@ CREATE TABLE `seq_region_synonym` (
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
   UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -725,22 +725,22 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=95700 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -781,12 +781,12 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=21742 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,18 +817,18 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=21742 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,41 +836,41 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
   KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1000000 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
index 6096f9d767..11658fd075 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:34 2015
+-- Created on Fri May  6 15:44:14 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -270,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -328,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -584,7 +584,7 @@ CREATE UNIQUE INDEX c02 ON misc_set (code);
 CREATE TABLE object_xref (
   object_xref_id integer NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
-  ensembl_object_type enum NOT NULL,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
   analysis_id smallint NOT NULL
@@ -615,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -633,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -856,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -907,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -936,7 +936,8 @@ CREATE TABLE unmapped_object (
   query_score double precision,
   target_score double precision,
   ensembl_id integer DEFAULT 0,
-  ensembl_object_type enum DEFAULT 'RawContig'
+  ensembl_object_type enum DEFAULT 'RawContig',
+  parent varchar(255)
 );
 
 --
@@ -953,7 +954,7 @@ CREATE TABLE unmapped_reason (
 --
 CREATE TABLE xref (
   xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  external_db_id integer NOT NULL DEFAULT 0,
+  external_db_id integer NOT NULL,
   dbprimary_acc varchar(512) NOT NULL,
   display_label varchar(512) NOT NULL,
   version varchar(10),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
index 0473ad2145..10e58422b2 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/meta.txt
@@ -73,3 +73,4 @@
 122	\N	patch	patch_83_84_b.sql|xref.version_default
 123	\N	patch	patch_83_84_c.sql|protein_feature_unique
 124	\N	patch	patch_83_84_d.sql|longer_synonym
+125	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index ebd656a1de..00154a2133 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -21,27 +21,27 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -73,7 +73,7 @@ CREATE TABLE `assembly_exception` (
   PRIMARY KEY (`assembly_exception_id`),
   KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
   KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `associated_group` (
   `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=8 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -151,7 +151,7 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,7 +236,7 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -300,11 +300,11 @@ CREATE TABLE `gene` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=126 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,9 +500,9 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
@@ -511,9 +511,9 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -656,9 +656,9 @@ CREATE TABLE `protein_feature` (
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
@@ -686,18 +686,18 @@ CREATE TABLE `repeat_feature` (
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -717,7 +717,7 @@ CREATE TABLE `seq_region_synonym` (
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
   UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -725,7 +725,7 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
@@ -735,12 +735,12 @@ CREATE TABLE `simple_feature` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -786,7 +786,7 @@ CREATE TABLE `transcript` (
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,7 +817,7 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
@@ -828,7 +828,7 @@ CREATE TABLE `translation` (
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,20 +854,20 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
index ce2a080b9e..0f982fa109 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:45 2015
+-- Created on Fri May  6 15:44:32 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -270,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -328,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -615,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -633,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -856,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -907,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
index dc142d54f4..ff7d5c3720 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/meta.txt
@@ -78,3 +78,4 @@
 2085	\N	patch	patch_83_84_b.sql|xref.version_default
 2086	\N	patch	patch_83_84_c.sql|protein_feature_unique
 2087	\N	patch	patch_83_84_d.sql|longer_synonym
+2088	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
index ebd656a1de..abe3568304 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
@@ -5,7 +5,7 @@ CREATE TABLE `alt_allele` (
   PRIMARY KEY (`alt_allele_id`),
   UNIQUE KEY `gene_idx` (`gene_id`),
   KEY `gene_id` (`gene_id`,`alt_allele_group_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `alt_allele_attrib` (
   `alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,32 +16,32 @@ CREATE TABLE `alt_allele_attrib` (
 CREATE TABLE `alt_allele_group` (
   `alt_allele_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   PRIMARY KEY (`alt_allele_group_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=5213 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=8449 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -73,7 +73,7 @@ CREATE TABLE `assembly_exception` (
   PRIMARY KEY (`assembly_exception_id`),
   KEY `sr_idx` (`seq_region_id`,`seq_region_start`),
   KEY `ex_idx` (`exc_seq_region_id`,`exc_seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=155 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `associated_group` (
   `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=405 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1004 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -144,17 +144,17 @@ CREATE TABLE `density_feature` (
   PRIMARY KEY (`density_feature_id`),
   KEY `seq_region_idx` (`density_type_id`,`seq_region_id`,`seq_region_start`),
   KEY `seq_region_id_idx` (`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=16758826 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `density_type` (
   `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=110 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -172,7 +172,7 @@ CREATE TABLE `ditag` (
   `tag_count` smallint(6) DEFAULT '1',
   `sequence` text,
   PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1366612 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `ditag_feature` (
   `ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -191,11 +191,11 @@ CREATE TABLE `ditag_feature` (
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
   KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1221449 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -223,7 +223,7 @@ CREATE TABLE `dna_align_feature` (
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=29387404 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `exon` (
   `exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -236,13 +236,13 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=7296966 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -297,14 +297,14 @@ CREATE TABLE `gene` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=633706 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -332,7 +332,7 @@ CREATE TABLE `genome_statistics` (
   PRIMARY KEY (`genome_statistics_id`),
   UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
   KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `identity_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,29 +376,29 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=852 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=394 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_set` (
   `mapping_set_id` int(10) unsigned NOT NULL,
@@ -411,15 +411,15 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=27 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
   `marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -432,14 +432,14 @@ CREATE TABLE `marker_feature` (
   PRIMARY KEY (`marker_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=27 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,12 +448,12 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=716771 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2089 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -489,7 +489,7 @@ CREATE TABLE `misc_feature` (
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=93001 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_feature_misc_set` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -500,25 +500,25 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
   KEY `xref_idx` (`xref_id`,`ensembl_object_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=17375428 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `ontology_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,11 +574,11 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=250655 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_exon` (
   `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -594,7 +594,7 @@ CREATE TABLE `prediction_exon` (
   PRIMARY KEY (`prediction_exon_id`),
   KEY `prediction_transcript_id` (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=394607 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_transcript` (
   `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -603,11 +603,11 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=54799 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `protein_align_feature` (
   `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -631,7 +631,7 @@ CREATE TABLE `protein_align_feature` (
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=19573639 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `protein_feature` (
   `protein_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -652,20 +652,20 @@ CREATE TABLE `protein_feature` (
   KEY `translation_id` (`translation_id`),
   KEY `hitname_index` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=7821872 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
   KEY `class` (`repeat_class`),
   KEY `consensus` (`repeat_consensus`(10)),
   KEY `type` (`repeat_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=595635 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_feature` (
   `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,22 +682,22 @@ CREATE TABLE `repeat_feature` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `repeat_idx` (`repeat_consensus_id`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=31576665 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1001161224 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -717,7 +717,7 @@ CREATE TABLE `seq_region_synonym` (
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
   UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=177 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -725,22 +725,22 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=968471 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -781,12 +781,12 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2047756 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,18 +817,18 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1044748 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,41 +836,41 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=12401901 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
   KEY `info_type_idx` (`info_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=7795492 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql
index 5ec73bfc0b..abccb33bd8 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/SQLite/table.sql
@@ -1,3 +1,784 @@
+-- 
+-- Created by SQL::Translator::Producer::SQLite
+-- Created on Fri May  6 15:44:47 2016
+-- 
+
 BEGIN TRANSACTION;
 
+--
+-- Table: allele
+--
+CREATE TABLE allele (
+  allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  allele_code_id integer NOT NULL,
+  population_id integer,
+  frequency float,
+  count integer,
+  frequency_submitter_handle integer
+);
+
+--
+-- Table: allele_code
+--
+CREATE TABLE allele_code (
+  allele_code_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  allele varchar(255)
+);
+
+CREATE UNIQUE INDEX allele_idx ON allele_code (allele);
+
+--
+-- Table: associate_study
+--
+CREATE TABLE associate_study (
+  study1_id integer NOT NULL,
+  study2_id integer NOT NULL,
+  PRIMARY KEY (study1_id, study2_id)
+);
+
+--
+-- Table: attrib
+--
+CREATE TABLE attrib (
+  attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  attrib_type_id smallint NOT NULL DEFAULT 0,
+  value text NOT NULL
+);
+
+CREATE UNIQUE INDEX type_val_idx ON attrib (attrib_type_id, value);
+
+--
+-- Table: attrib_set
+--
+CREATE TABLE attrib_set (
+  attrib_set_id integer NOT NULL DEFAULT 0,
+  attrib_id integer NOT NULL DEFAULT 0
+);
+
+CREATE UNIQUE INDEX set_idx ON attrib_set (attrib_set_id, attrib_id);
+
+--
+-- Table: attrib_type
+--
+CREATE TABLE attrib_type (
+  attrib_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  code varchar(20) NOT NULL DEFAULT '',
+  name varchar(255) NOT NULL DEFAULT '',
+  description text
+);
+
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+
+--
+-- Table: compressed_genotype_region
+--
+CREATE TABLE compressed_genotype_region (
+  sample_id integer NOT NULL,
+  seq_region_id integer NOT NULL,
+  seq_region_start integer NOT NULL,
+  seq_region_end integer NOT NULL,
+  seq_region_strand tinyint NOT NULL,
+  genotypes blob
+);
+
+--
+-- Table: compressed_genotype_var
+--
+CREATE TABLE compressed_genotype_var (
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  genotypes blob
+);
+
+--
+-- Table: coord_system
+--
+CREATE TABLE coord_system (
+  coord_system_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  species_id integer NOT NULL DEFAULT 1,
+  name varchar(40) NOT NULL,
+  version varchar(255),
+  rank integer NOT NULL,
+  attrib varchar
+);
+
+CREATE UNIQUE INDEX name_idx ON coord_system (name, version, species_id);
+
+CREATE UNIQUE INDEX rank_idx ON coord_system (rank, species_id);
+
+--
+-- Table: display_group
+--
+CREATE TABLE display_group (
+  display_group_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  display_priority integer NOT NULL,
+  display_name varchar(255) NOT NULL
+);
+
+CREATE UNIQUE INDEX display_name ON display_group (display_name);
+
+CREATE UNIQUE INDEX display_priority ON display_group (display_priority);
+
+--
+-- Table: failed_allele
+--
+CREATE TABLE failed_allele (
+  failed_allele_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  allele_id integer NOT NULL,
+  failed_description_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX allele_idx02 ON failed_allele (allele_id, failed_description_id);
+
+--
+-- Table: failed_description
+--
+CREATE TABLE failed_description (
+  failed_description_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  description text NOT NULL
+);
+
+--
+-- Table: failed_structural_variation
+--
+CREATE TABLE failed_structural_variation (
+  failed_structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  structural_variation_id integer NOT NULL,
+  failed_description_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX structural_variation_idx ON failed_structural_variation (structural_variation_id, failed_description_id);
+
+--
+-- Table: failed_variation
+--
+CREATE TABLE failed_variation (
+  failed_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  failed_description_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX variation_idx ON failed_variation (variation_id, failed_description_id);
+
+--
+-- Table: genotype_code
+--
+CREATE TABLE genotype_code (
+  genotype_code_id integer NOT NULL,
+  allele_code_id integer NOT NULL,
+  haplotype_id tinyint NOT NULL,
+  phased tinyint
+);
+
+--
+-- Table: individual
+--
+CREATE TABLE individual (
+  individual_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255),
+  description text,
+  gender enum NOT NULL DEFAULT 'Unknown',
+  father_individual_id integer,
+  mother_individual_id integer,
+  individual_type_id integer NOT NULL DEFAULT 0
+);
+
+--
+-- Table: individual_synonym
+--
+CREATE TABLE individual_synonym (
+  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  individual_id integer NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
+--
+-- Table: individual_type
+--
+CREATE TABLE individual_type (
+  individual_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255) NOT NULL,
+  description text
+);
+
+--
+-- Table: meta
+--
+CREATE TABLE meta (
+  meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  species_id integer DEFAULT 1,
+  meta_key varchar(40) NOT NULL,
+  meta_value varchar(255) NOT NULL
+);
+
+CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
+
+--
+-- Table: meta_coord
+--
+CREATE TABLE meta_coord (
+  table_name varchar(40) NOT NULL,
+  coord_system_id integer NOT NULL,
+  max_length integer
+);
+
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+
+--
+-- Table: motif_feature_variation
+--
+CREATE TABLE motif_feature_variation (
+  motif_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_feature_id integer NOT NULL,
+  feature_stable_id varchar(128),
+  motif_feature_id integer NOT NULL,
+  allele_string text,
+  somatic tinyint NOT NULL DEFAULT 0,
+  consequence_types varchar,
+  motif_name text,
+  motif_start integer,
+  motif_end integer,
+  motif_score_delta float,
+  in_informative_position tinyint NOT NULL DEFAULT 0
+);
+
+--
+-- Table: phenotype
+--
+CREATE TABLE phenotype (
+  phenotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  stable_id varchar(255),
+  name varchar(50),
+  description varchar(255)
+);
+
+CREATE UNIQUE INDEX desc_idx ON phenotype (description);
+
+--
+-- Table: phenotype_feature
+--
+CREATE TABLE phenotype_feature (
+  phenotype_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  phenotype_id integer,
+  source_id integer,
+  study_id integer,
+  type enum,
+  object_id varchar(255),
+  is_significant tinyint DEFAULT 1,
+  seq_region_id integer,
+  seq_region_start integer,
+  seq_region_end integer,
+  seq_region_strand tinyint
+);
+
+--
+-- Table: phenotype_feature_attrib
+--
+CREATE TABLE phenotype_feature_attrib (
+  phenotype_feature_id integer NOT NULL,
+  attrib_type_id integer,
+  value varchar(255)
+);
+
+--
+-- Table: population
+--
+CREATE TABLE population (
+  population_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255),
+  size integer,
+  description text,
+  collection tinyint DEFAULT 0,
+  freqs_from_gts tinyint,
+  display enum DEFAULT 'UNDISPLAYABLE',
+  display_group_id tinyint
+);
+
+--
+-- Table: population_genotype
+--
+CREATE TABLE population_genotype (
+  population_genotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  genotype_code_id integer,
+  frequency float,
+  population_id integer,
+  count integer
+);
+
+--
+-- Table: population_structure
+--
+CREATE TABLE population_structure (
+  super_population_id integer NOT NULL,
+  sub_population_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX super_population_idx ON population_structure (super_population_id, sub_population_id);
+
+--
+-- Table: population_synonym
+--
+CREATE TABLE population_synonym (
+  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  population_id integer NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
+--
+-- Table: protein_function_predictions
+--
+CREATE TABLE protein_function_predictions (
+  translation_md5_id integer NOT NULL,
+  analysis_attrib_id integer NOT NULL,
+  prediction_matrix mediumblob,
+  PRIMARY KEY (translation_md5_id, analysis_attrib_id)
+);
+
+--
+-- Table: protein_function_predictions_attrib
+--
+CREATE TABLE protein_function_predictions_attrib (
+  translation_md5_id integer NOT NULL,
+  analysis_attrib_id integer NOT NULL,
+  attrib_type_id integer NOT NULL,
+  position_values blob,
+  PRIMARY KEY (translation_md5_id, analysis_attrib_id, attrib_type_id)
+);
+
+--
+-- Table: publication
+--
+CREATE TABLE publication (
+  publication_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  title varchar(255),
+  authors varchar(255),
+  pmid integer,
+  pmcid varchar(255),
+  year integer,
+  doi varchar(50),
+  ucsc_id varchar(50)
+);
+
+--
+-- Table: read_coverage
+--
+CREATE TABLE read_coverage (
+  seq_region_id integer NOT NULL,
+  seq_region_start integer NOT NULL,
+  seq_region_end integer NOT NULL,
+  level tinyint NOT NULL,
+  sample_id integer NOT NULL
+);
+
+--
+-- Table: regulatory_feature_variation
+--
+CREATE TABLE regulatory_feature_variation (
+  regulatory_feature_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_feature_id integer NOT NULL,
+  feature_stable_id varchar(128),
+  feature_type text,
+  allele_string text,
+  somatic tinyint NOT NULL DEFAULT 0,
+  consequence_types varchar
+);
+
+--
+-- Table: sample
+--
+CREATE TABLE sample (
+  sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  individual_id integer NOT NULL,
+  name varchar(255),
+  description text,
+  study_id integer,
+  display enum DEFAULT 'UNDISPLAYABLE',
+  has_coverage tinyint NOT NULL DEFAULT 0,
+  variation_set_id varchar
+);
+
+--
+-- Table: sample_genotype_multiple_bp
+--
+CREATE TABLE sample_genotype_multiple_bp (
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  allele_1 varchar(255),
+  allele_2 varchar(255),
+  sample_id integer
+);
+
+--
+-- Table: sample_population
+--
+CREATE TABLE sample_population (
+  sample_id integer NOT NULL,
+  population_id integer NOT NULL
+);
+
+--
+-- Table: sample_synonym
+--
+CREATE TABLE sample_synonym (
+  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  sample_id integer NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
+--
+-- Table: seq_region
+--
+CREATE TABLE seq_region (
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(40) NOT NULL,
+  coord_system_id integer NOT NULL
+);
+
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+
+--
+-- Table: source
+--
+CREATE TABLE source (
+  source_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(24) NOT NULL,
+  version integer,
+  description varchar(255),
+  url varchar(255),
+  type enum,
+  somatic_status enum DEFAULT 'germline',
+  data_types varchar
+);
+
+--
+-- Table: strain_gtype_poly
+--
+CREATE TABLE strain_gtype_poly (
+  variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  sample_name varchar(100)
+);
+
+--
+-- Table: structural_variation
+--
+CREATE TABLE structural_variation (
+  structural_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_name varchar(255),
+  alias varchar(255),
+  source_id integer NOT NULL,
+  study_id integer,
+  class_attrib_id integer NOT NULL DEFAULT 0,
+  clinical_significance varchar,
+  validation_status enum,
+  is_evidence tinyint DEFAULT 0,
+  somatic tinyint NOT NULL DEFAULT 0,
+  copy_number tinyint
+);
+
+CREATE UNIQUE INDEX variation_name ON structural_variation (variation_name);
+
+--
+-- Table: structural_variation_association
+--
+CREATE TABLE structural_variation_association (
+  structural_variation_id integer NOT NULL,
+  supporting_structural_variation_id integer NOT NULL,
+  PRIMARY KEY (structural_variation_id, supporting_structural_variation_id)
+);
+
+--
+-- Table: structural_variation_feature
+--
+CREATE TABLE structural_variation_feature (
+  structural_variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  seq_region_id integer NOT NULL,
+  outer_start integer,
+  seq_region_start integer NOT NULL,
+  inner_start integer,
+  inner_end integer,
+  seq_region_end integer NOT NULL,
+  outer_end integer,
+  seq_region_strand tinyint NOT NULL,
+  structural_variation_id integer NOT NULL,
+  variation_name varchar(255),
+  source_id integer NOT NULL,
+  study_id integer,
+  class_attrib_id integer NOT NULL DEFAULT 0,
+  allele_string longtext,
+  is_evidence tinyint NOT NULL DEFAULT 0,
+  somatic tinyint NOT NULL DEFAULT 0,
+  breakpoint_order tinyint,
+  length integer,
+  variation_set_id varchar NOT NULL DEFAULT ''
+);
+
+--
+-- Table: structural_variation_sample
+--
+CREATE TABLE structural_variation_sample (
+  structural_variation_sample_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  structural_variation_id integer NOT NULL,
+  sample_id integer,
+  strain_id integer
+);
+
+--
+-- Table: study
+--
+CREATE TABLE study (
+  study_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255),
+  description text,
+  url varchar(255),
+  external_reference varchar(255),
+  study_type varchar(255)
+);
+
+--
+-- Table: submitter_handle
+--
+CREATE TABLE submitter_handle (
+  handle_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  handle varchar(25)
+);
+
+CREATE UNIQUE INDEX handle ON submitter_handle (handle);
+
+--
+-- Table: subsnp_handle
+--
+CREATE TABLE subsnp_handle (
+  subsnp_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  handle varchar(20)
+);
+
+--
+-- Table: subsnp_map
+--
+CREATE TABLE subsnp_map (
+  variation_id integer NOT NULL,
+  subsnp_id integer NOT NULL,
+  PRIMARY KEY (variation_id, subsnp_id)
+);
+
+--
+-- Table: tmp_individual_genotype_single_bp
+--
+CREATE TABLE tmp_individual_genotype_single_bp (
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  allele_1 char(1),
+  allele_2 char(1),
+  individual_id integer
+);
+
+--
+-- Table: transcript_variation
+--
+CREATE TABLE transcript_variation (
+  transcript_variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_feature_id integer NOT NULL,
+  feature_stable_id varchar(128),
+  allele_string text,
+  somatic tinyint NOT NULL DEFAULT 0,
+  consequence_types varchar,
+  cds_start integer,
+  cds_end integer,
+  cdna_start integer,
+  cdna_end integer,
+  translation_start integer,
+  translation_end integer,
+  distance_to_transcript integer,
+  codon_allele_string text,
+  pep_allele_string text,
+  hgvs_genomic text,
+  hgvs_transcript text,
+  hgvs_protein text,
+  polyphen_prediction enum,
+  polyphen_score float,
+  sift_prediction enum,
+  sift_score float,
+  display integer DEFAULT 1
+);
+
+--
+-- Table: translation_md5
+--
+CREATE TABLE translation_md5 (
+  translation_md5_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  translation_md5 char(32) NOT NULL
+);
+
+CREATE UNIQUE INDEX md5_idx ON translation_md5 (translation_md5);
+
+--
+-- Table: variation
+--
+CREATE TABLE variation (
+  variation_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255),
+  ancestral_allele varchar(255),
+  flipped tinyint,
+  class_attrib_id integer DEFAULT 0,
+  somatic tinyint NOT NULL DEFAULT 0,
+  minor_allele varchar(50),
+  minor_allele_freq float,
+  minor_allele_count integer,
+  clinical_significance varchar,
+  evidence_attribs varchar,
+  display integer DEFAULT 1
+);
+
+CREATE UNIQUE INDEX name ON variation (name);
+
+--
+-- Table: variation_attrib
+--
+CREATE TABLE variation_attrib (
+  variation_id integer NOT NULL,
+  attrib_id integer,
+  value varchar(255)
+);
+
+--
+-- Table: variation_citation
+--
+CREATE TABLE variation_citation (
+  variation_id integer NOT NULL,
+  publication_id integer NOT NULL,
+  PRIMARY KEY (variation_id, publication_id)
+);
+
+--
+-- Table: variation_feature
+--
+CREATE TABLE variation_feature (
+  variation_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  seq_region_id integer NOT NULL,
+  seq_region_start integer NOT NULL,
+  seq_region_end integer NOT NULL,
+  seq_region_strand tinyint NOT NULL,
+  variation_id integer NOT NULL,
+  allele_string varchar(50000),
+  variation_name varchar(255),
+  map_weight integer NOT NULL,
+  flags varchar,
+  source_id integer NOT NULL,
+  consequence_types varchar NOT NULL DEFAULT 'intergenic_variant',
+  variation_set_id varchar NOT NULL DEFAULT '',
+  class_attrib_id integer DEFAULT 0,
+  somatic tinyint NOT NULL DEFAULT 0,
+  minor_allele varchar(50),
+  minor_allele_freq float,
+  minor_allele_count integer,
+  alignment_quality double precision,
+  clinical_significance varchar,
+  evidence_attribs varchar,
+  display integer DEFAULT 1
+);
+
+--
+-- Table: variation_feature_bak
+--
+CREATE TABLE variation_feature_bak (
+  variation_feature_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL,
+  seq_region_start integer NOT NULL,
+  seq_region_end integer NOT NULL,
+  seq_region_strand tinyint NOT NULL,
+  variation_id integer NOT NULL,
+  allele_string varchar(50000),
+  variation_name varchar(255),
+  map_weight integer NOT NULL,
+  flags varchar,
+  source_id integer NOT NULL,
+  validation_status varchar,
+  consequence_types varchar NOT NULL DEFAULT 'intergenic_variant',
+  variation_set_id varchar NOT NULL DEFAULT '',
+  class_attrib_id integer DEFAULT 0,
+  somatic tinyint NOT NULL DEFAULT 0,
+  minor_allele varchar(50),
+  minor_allele_freq float,
+  minor_allele_count integer,
+  alignment_quality double precision,
+  evidence varchar
+);
+
+--
+-- Table: variation_genename
+--
+CREATE TABLE variation_genename (
+  variation_id integer NOT NULL,
+  gene_name varchar(255) NOT NULL,
+  PRIMARY KEY (variation_id, gene_name)
+);
+
+--
+-- Table: variation_hgvs
+--
+CREATE TABLE variation_hgvs (
+  variation_id integer NOT NULL,
+  hgvs_name varchar(255) NOT NULL,
+  PRIMARY KEY (variation_id, hgvs_name)
+);
+
+--
+-- Table: variation_set
+--
+CREATE TABLE variation_set (
+  variation_set_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  name varchar(255),
+  description text,
+  short_name_attrib_id integer
+);
+
+--
+-- Table: variation_set_structural_variation
+--
+CREATE TABLE variation_set_structural_variation (
+  structural_variation_id integer NOT NULL,
+  variation_set_id integer NOT NULL,
+  PRIMARY KEY (structural_variation_id, variation_set_id)
+);
+
+--
+-- Table: variation_set_structure
+--
+CREATE TABLE variation_set_structure (
+  variation_set_super integer NOT NULL,
+  variation_set_sub integer NOT NULL,
+  PRIMARY KEY (variation_set_super, variation_set_sub)
+);
+
+--
+-- Table: variation_set_variation
+--
+CREATE TABLE variation_set_variation (
+  variation_id integer NOT NULL,
+  variation_set_id integer NOT NULL,
+  PRIMARY KEY (variation_id, variation_set_id)
+);
+
+--
+-- Table: variation_synonym
+--
+CREATE TABLE variation_synonym (
+  variation_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  variation_id integer NOT NULL,
+  subsnp_id integer,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
+CREATE UNIQUE INDEX name02 ON variation_synonym (name, source_id);
+
 COMMIT;
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
index a1df78dac3..c74377868b 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/meta.txt
@@ -1,3 +1,8 @@
 1	\N	schema_type	variation
-2	\N	schema_version	84
+2	\N	schema_version	85
 3	\N	patch	patch_83_84_a.sql|schema version
+4	\N	patch	patch_84_85_a.sql|schema version
+5	\N	patch	patch_84_85_b.sql|create sample_synonym
+6	\N	patch	patch_84_85_c.sql|drop column moltype from variation_synonym
+7	\N	patch	patch_85_86_d.sql|Making attrib_id auto_increment
+8	\N	patch	patch_85_86_e.sql|drop the table tagged_variation_feature
diff --git a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
index e355b43dff..887adf9308 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/variation/table.sql
@@ -11,13 +11,13 @@ CREATE TABLE `allele` (
   KEY `variation_idx` (`variation_id`),
   KEY `subsnp_idx` (`subsnp_id`),
   KEY `population_idx` (`population_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `allele_code` (
   `allele_code_id` int(11) NOT NULL AUTO_INCREMENT,
   `allele` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`allele_code_id`),
-  UNIQUE KEY `allele_idx` (`allele`(255))
+  UNIQUE KEY `allele_idx` (`allele`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `associate_study` (
@@ -27,12 +27,12 @@ CREATE TABLE `associate_study` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `attrib` (
-  `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
+  `attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
   `value` text NOT NULL,
   PRIMARY KEY (`attrib_id`),
   UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=422 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `attrib_set` (
   `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
@@ -158,7 +158,7 @@ CREATE TABLE `individual_type` (
   `name` varchar(255) NOT NULL,
   `description` text,
   PRIMARY KEY (`individual_type_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta` (
   `meta_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -168,7 +168,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -205,7 +205,7 @@ CREATE TABLE `phenotype` (
   UNIQUE KEY `desc_idx` (`description`),
   KEY `stable_idx` (`stable_id`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `phenotype_feature` (
   `phenotype_feature_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
@@ -225,7 +225,7 @@ CREATE TABLE `phenotype_feature` (
   KEY `type_idx` (`type`),
   KEY `pos_idx` (`seq_region_id`,`seq_region_start`,`seq_region_end`),
   KEY `source_idx` (`source_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `phenotype_feature_attrib` (
   `phenotype_feature_id` int(11) unsigned NOT NULL,
@@ -246,7 +246,7 @@ CREATE TABLE `population` (
   `display_group_id` tinyint(1) DEFAULT NULL,
   PRIMARY KEY (`population_id`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `population_genotype` (
   `population_genotype_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -362,6 +362,16 @@ CREATE TABLE `sample_population` (
   KEY `sample_idx` (`sample_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
+CREATE TABLE `sample_synonym` (
+  `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `sample_id` int(10) unsigned NOT NULL,
+  `source_id` int(10) unsigned NOT NULL,
+  `name` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`synonym_id`),
+  KEY `sample_idx` (`sample_id`),
+  KEY `name` (`name`,`source_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL,
   `name` varchar(40) NOT NULL,
@@ -381,7 +391,7 @@ CREATE TABLE `source` (
   `somatic_status` enum('germline','somatic','mixed') DEFAULT 'germline',
   `data_types` set('variation','variation_synonym','structural_variation','phenotype_feature','study') DEFAULT NULL,
   PRIMARY KEY (`source_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `strain_gtype_poly` (
   `variation_id` int(10) unsigned NOT NULL,
@@ -406,7 +416,7 @@ CREATE TABLE `structural_variation` (
   KEY `source_idx` (`source_id`),
   KEY `study_idx` (`study_id`),
   KEY `attrib_idx` (`class_attrib_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `structural_variation_association` (
   `structural_variation_id` int(10) unsigned NOT NULL,
@@ -444,7 +454,7 @@ CREATE TABLE `structural_variation_feature` (
   KEY `study_idx` (`study_id`),
   KEY `attrib_idx` (`class_attrib_id`),
   KEY `variation_set_idx` (`variation_set_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `structural_variation_sample` (
   `structural_variation_sample_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -467,7 +477,7 @@ CREATE TABLE `study` (
   `study_type` varchar(255) DEFAULT NULL,
   PRIMARY KEY (`study_id`),
   KEY `source_idx` (`source_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `submitter_handle` (
   `handle_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -489,15 +499,6 @@ CREATE TABLE `subsnp_map` (
   KEY `variation_idx` (`variation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
-CREATE TABLE `tagged_variation_feature` (
-  `variation_feature_id` int(10) unsigned NOT NULL,
-  `tagged_variation_feature_id` int(10) unsigned DEFAULT NULL,
-  `population_id` int(10) unsigned NOT NULL,
-  KEY `tag_idx` (`variation_feature_id`),
-  KEY `tagged_idx` (`tagged_variation_feature_id`),
-  KEY `population_idx` (`population_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-
 CREATE TABLE `tmp_individual_genotype_single_bp` (
   `variation_id` int(10) NOT NULL,
   `subsnp_id` int(15) unsigned DEFAULT NULL,
@@ -563,7 +564,7 @@ CREATE TABLE `variation` (
   PRIMARY KEY (`variation_id`),
   UNIQUE KEY `name` (`name`),
   KEY `source_idx` (`source_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `variation_attrib` (
   `variation_id` int(11) unsigned NOT NULL,
@@ -608,7 +609,7 @@ CREATE TABLE `variation_feature` (
   KEY `variation_set_idx` (`variation_set_id`),
   KEY `consequence_type_idx` (`consequence_types`),
   KEY `source_idx` (`source_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `variation_feature_bak` (
   `variation_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -653,7 +654,7 @@ CREATE TABLE `variation_set` (
   `short_name_attrib_id` int(10) unsigned DEFAULT NULL,
   PRIMARY KEY (`variation_set_id`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `variation_set_structural_variation` (
   `structural_variation_id` int(10) unsigned NOT NULL,
@@ -681,7 +682,6 @@ CREATE TABLE `variation_synonym` (
   `subsnp_id` int(15) unsigned DEFAULT NULL,
   `source_id` int(10) unsigned NOT NULL,
   `name` varchar(255) DEFAULT NULL,
-  `moltype` varchar(50) DEFAULT NULL,
   PRIMARY KEY (`variation_synonym_id`),
   UNIQUE KEY `name` (`name`,`source_id`),
   KEY `variation_idx` (`variation_id`),
diff --git a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
index d5c8686d70..f36902d0a1 100644
--- a/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:18:55 2015
+-- Created on Fri May  6 15:45:03 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float(8,2) NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL,
-  type varchar(30) NOT NULL,
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,11 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -303,14 +301,12 @@ CREATE TABLE external_db (
   description text
 );
 
-CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
-
 --
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -380,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -396,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -418,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -437,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -471,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -484,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -496,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -510,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -522,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -531,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -577,24 +573,24 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
@@ -605,7 +601,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -619,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -637,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -664,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -680,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -693,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -714,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision(8,2),
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -735,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -746,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -762,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -796,7 +792,7 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
 CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
@@ -806,12 +802,12 @@ CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -824,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -860,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -911,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -933,7 +929,7 @@ CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, a
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -944,8 +940,6 @@ CREATE TABLE unmapped_object (
   parent varchar(255)
 );
 
-CREATE UNIQUE INDEX unique_unmapped_obj_idx ON unmapped_object (ensembl_id, ensembl_object_type, identifier, unmapped_reason_id, parent, external_db_id);
-
 --
 -- Table: unmapped_reason
 --
diff --git a/modules/t/test-genome-DBs/mapping/core/meta.txt b/modules/t/test-genome-DBs/mapping/core/meta.txt
index 34a482d153..bf9db054d2 100644
--- a/modules/t/test-genome-DBs/mapping/core/meta.txt
+++ b/modules/t/test-genome-DBs/mapping/core/meta.txt
@@ -11,7 +11,7 @@
 11	\N	patch	patch_74_75_d.sql|default_transcript_source
 12	\N	patch	patch_74_75_e.sql|unique_attrib_key
 13	\N	patch	patch_74_75_f.sql|longer_code
-107	0		\N
+107	0		
 108	\N	patch	patch_75_76_a.sql|schema_version
 109	\N	patch	patch_75_76_b.sql|allow_null_karyotype
 110	\N	patch	patch_75_76_c.sql|remove_alternative_splicing
@@ -34,3 +34,4 @@
 127	\N	patch	patch_83_84_b.sql|xref.version_default
 128	\N	patch	patch_83_84_c.sql|protein_feature_unique
 129	\N	patch	patch_83_84_d.sql|longer_synonym
+130	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/mapping/core/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index ebd656a1de..6ec8041323 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/table.sql
@@ -21,18 +21,18 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
@@ -41,7 +41,7 @@ CREATE TABLE `analysis` (
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -151,7 +151,7 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,7 +236,7 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -300,11 +300,11 @@ CREATE TABLE `gene` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=131 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,9 +500,9 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
@@ -511,9 +511,9 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -656,9 +656,9 @@ CREATE TABLE `protein_feature` (
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
@@ -686,18 +686,18 @@ CREATE TABLE `repeat_feature` (
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -725,7 +725,7 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
@@ -735,12 +735,12 @@ CREATE TABLE `simple_feature` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -786,7 +786,7 @@ CREATE TABLE `transcript` (
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,7 +817,7 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
@@ -828,7 +828,7 @@ CREATE TABLE `translation` (
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,20 +854,20 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
index 3c6ed03eea..b64a483a8b 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:19:05 2015
+-- Created on Fri May  6 15:45:20 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL DEFAULT '',
-  type varchar(30) NOT NULL DEFAULT '',
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,13 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  dbprimary_acc_linkable tinyint NOT NULL DEFAULT 1,
-  display_label_linkable tinyint NOT NULL DEFAULT 0,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -309,8 +305,8 @@ CREATE TABLE external_db (
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -360,6 +356,8 @@ CREATE TABLE gene_attrib (
   value text NOT NULL
 );
 
+CREATE UNIQUE INDEX gene_attribx ON gene_attrib (gene_id, attrib_type_id, value);
+
 --
 -- Table: genome_statistics
 --
@@ -378,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -394,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -416,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -435,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -469,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -482,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -494,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -508,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -520,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -529,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -545,6 +543,8 @@ CREATE TABLE misc_attrib (
   value text NOT NULL
 );
 
+CREATE UNIQUE INDEX misc_attribx ON misc_attrib (misc_feature_id, attrib_type_id, value);
+
 --
 -- Table: misc_feature
 --
@@ -573,35 +573,35 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
 --
 CREATE TABLE ontology_xref (
   object_xref_id integer NOT NULL DEFAULT 0,
-  source_xref_id integer,
-  linkage_type varchar(3)
+  linkage_type varchar(3),
+  source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -615,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -633,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -660,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -676,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -689,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -710,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision,
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -731,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -742,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -758,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -774,6 +774,8 @@ CREATE TABLE seq_region_attrib (
   value text NOT NULL
 );
 
+CREATE UNIQUE INDEX region_attribx ON seq_region_attrib (seq_region_id, attrib_type_id, value);
+
 --
 -- Table: seq_region_mapping
 --
@@ -790,22 +792,22 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
-CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym);
+CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 
 --
 -- Table: simple_feature
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -818,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -854,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -870,6 +872,8 @@ CREATE TABLE transcript_attrib (
   value text NOT NULL
 );
 
+CREATE UNIQUE INDEX transcript_attribx ON transcript_attrib (transcript_id, attrib_type_id, value);
+
 --
 -- Table: transcript_intron_supporting_evidence
 --
@@ -903,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -917,13 +921,15 @@ CREATE TABLE translation_attrib (
   value text NOT NULL
 );
 
+CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, attrib_type_id, value);
+
 --
 -- Table: unmapped_object
 --
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -948,9 +954,9 @@ CREATE TABLE unmapped_reason (
 --
 CREATE TABLE xref (
   xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  external_db_id integer,
-  dbprimary_acc varchar(50) NOT NULL,
-  display_label varchar(128) NOT NULL,
+  external_db_id integer NOT NULL,
+  dbprimary_acc varchar(512) NOT NULL,
+  display_label varchar(512) NOT NULL,
   version varchar(10),
   description text,
   info_type enum NOT NULL DEFAULT 'NONE',
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
index ab40a22610..0c78bd9131 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/core/meta.txt
@@ -151,3 +151,4 @@
 1663	\N	patch	patch_83_84_b.sql|xref.version_default
 1664	\N	patch	patch_83_84_c.sql|protein_feature_unique
 1665	\N	patch	patch_83_84_d.sql|longer_synonym
+1666	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index ebd656a1de..27f6bfac4c 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
@@ -21,18 +21,18 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
@@ -41,7 +41,7 @@ CREATE TABLE `analysis` (
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=508 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=112 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -151,7 +151,7 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,7 +236,7 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -300,11 +300,11 @@ CREATE TABLE `gene` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=1667 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,9 +500,9 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
@@ -511,9 +511,9 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -656,9 +656,9 @@ CREATE TABLE `protein_feature` (
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
@@ -686,18 +686,18 @@ CREATE TABLE `repeat_feature` (
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=20603 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -725,7 +725,7 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
@@ -735,12 +735,12 @@ CREATE TABLE `simple_feature` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -786,7 +786,7 @@ CREATE TABLE `transcript` (
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,7 +817,7 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
@@ -828,7 +828,7 @@ CREATE TABLE `translation` (
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,20 +854,20 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql b/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql
index 86c2653824..1b9077b9a8 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:19:14 2015
+-- Created on Fri May  6 15:45:33 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -42,7 +42,7 @@ CREATE TABLE associate_study (
 -- Table: attrib
 --
 CREATE TABLE attrib (
-  attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  attrib_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   attrib_type_id smallint NOT NULL DEFAULT 0,
   value text NOT NULL
 );
@@ -422,6 +422,16 @@ CREATE TABLE sample_population (
   population_id integer NOT NULL
 );
 
+--
+-- Table: sample_synonym
+--
+CREATE TABLE sample_synonym (
+  synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  sample_id integer NOT NULL,
+  source_id integer NOT NULL,
+  name varchar(255)
+);
+
 --
 -- Table: seq_region
 --
@@ -549,15 +559,6 @@ CREATE TABLE subsnp_map (
   subsnp_id integer
 );
 
---
--- Table: tagged_variation_feature
---
-CREATE TABLE tagged_variation_feature (
-  variation_feature_id integer NOT NULL,
-  tagged_variation_feature_id integer,
-  population_id integer NOT NULL
-);
-
 --
 -- Table: tmp_sample_genotype_single_bp
 --
@@ -738,8 +739,7 @@ CREATE TABLE variation_synonym (
   variation_id integer NOT NULL,
   subsnp_id integer,
   source_id integer NOT NULL,
-  name varchar(255),
-  moltype varchar(50)
+  name varchar(255)
 );
 
 CREATE UNIQUE INDEX name02 ON variation_synonym (name, source_id);
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
index 0309216d7d..8ac6203a6b 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/meta.txt
@@ -1,5 +1,5 @@
 1	\N	schema_type	variation
-2	\N	schema_version	84
+2	\N	schema_version	85
 6	1	species.production_name	mus_musculus
 15	1	web_config	sv_study#Keane 2011 (DGVa study estd118)#Keane 2011#estd118
 14	1	web_config	set#All failed variants#All failed variants#variation_set_fail_all#failed
@@ -28,3 +28,8 @@
 34	\N	patch	patch_82_83_b.sql|Add the evidence ExAC in variation and variation_feature
 35	\N	patch	patch_82_83_c.sql|Drop the column validation_status in variation and variation_feature
 36	\N	patch	patch_83_84_a.sql|schema version
+37	\N	patch	patch_84_85_a.sql|schema version
+38	\N	patch	patch_84_85_b.sql|create sample_synonym
+39	\N	patch	patch_84_85_c.sql|drop column moltype from variation_synonym
+40	\N	patch	patch_85_86_d.sql|Making attrib_id auto_increment
+41	\N	patch	patch_85_86_e.sql|drop the table tagged_variation_feature
diff --git a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
index ffa2e24570..f635e996e7 100644
--- a/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/variation/table.sql
@@ -27,12 +27,12 @@ CREATE TABLE `associate_study` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `attrib` (
-  `attrib_id` int(11) unsigned NOT NULL DEFAULT '0',
+  `attrib_id` int(11) unsigned NOT NULL AUTO_INCREMENT,
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
   `value` text NOT NULL,
   PRIMARY KEY (`attrib_id`),
   UNIQUE KEY `type_val_idx` (`attrib_type_id`,`value`(80))
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=419 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `attrib_set` (
   `attrib_set_id` int(11) unsigned NOT NULL DEFAULT '0',
@@ -168,7 +168,7 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=37 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=42 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `table_name` varchar(40) NOT NULL,
@@ -364,6 +364,16 @@ CREATE TABLE `sample_population` (
   KEY `sample_idx` (`sample_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
+CREATE TABLE `sample_synonym` (
+  `synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
+  `sample_id` int(10) unsigned NOT NULL,
+  `source_id` int(10) unsigned NOT NULL,
+  `name` varchar(255) DEFAULT NULL,
+  PRIMARY KEY (`synonym_id`),
+  KEY `sample_idx` (`sample_id`),
+  KEY `name` (`name`,`source_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL,
   `name` varchar(40) NOT NULL,
@@ -482,15 +492,6 @@ CREATE TABLE `subsnp_map` (
   KEY `variation_idx` (`variation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
-CREATE TABLE `tagged_variation_feature` (
-  `variation_feature_id` int(10) unsigned NOT NULL,
-  `tagged_variation_feature_id` int(10) unsigned DEFAULT NULL,
-  `population_id` int(10) unsigned NOT NULL,
-  KEY `tag_idx` (`variation_feature_id`),
-  KEY `tagged_idx` (`tagged_variation_feature_id`),
-  KEY `population_idx` (`population_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
-
 CREATE TABLE `tmp_sample_genotype_single_bp` (
   `variation_id` int(10) NOT NULL,
   `subsnp_id` int(15) unsigned DEFAULT NULL,
@@ -650,7 +651,6 @@ CREATE TABLE `variation_synonym` (
   `subsnp_id` int(15) unsigned DEFAULT NULL,
   `source_id` int(10) unsigned NOT NULL,
   `name` varchar(255) DEFAULT NULL,
-  `moltype` varchar(50) DEFAULT NULL,
   PRIMARY KEY (`variation_synonym_id`),
   UNIQUE KEY `name` (`name`,`source_id`),
   KEY `variation_idx` (`variation_id`),
diff --git a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
index 7796eb66fe..da72638f23 100644
--- a/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:19:24 2015
+-- Created on Fri May  6 15:45:48 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float(8,2) NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL,
-  type varchar(30) NOT NULL,
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,11 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -303,14 +301,12 @@ CREATE TABLE external_db (
   description text
 );
 
-CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
-
 --
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -380,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -396,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -418,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -437,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -471,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -484,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -496,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -510,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -522,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -531,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -577,24 +573,24 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
@@ -605,7 +601,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -619,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -637,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -664,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -680,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -693,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -714,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision(8,2),
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -735,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -746,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -762,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -796,7 +792,7 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
 CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
@@ -806,12 +802,12 @@ CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -824,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -860,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -911,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -933,7 +929,7 @@ CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, a
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -944,8 +940,6 @@ CREATE TABLE unmapped_object (
   parent varchar(255)
 );
 
-CREATE UNIQUE INDEX unique_unmapped_obj_idx ON unmapped_object (ensembl_id, ensembl_object_type, identifier, unmapped_reason_id, parent, external_db_id);
-
 --
 -- Table: unmapped_reason
 --
diff --git a/modules/t/test-genome-DBs/nameless/core/meta.txt b/modules/t/test-genome-DBs/nameless/core/meta.txt
index 6cb205f59e..1c9d944bb6 100644
--- a/modules/t/test-genome-DBs/nameless/core/meta.txt
+++ b/modules/t/test-genome-DBs/nameless/core/meta.txt
@@ -72,3 +72,4 @@
 126	\N	patch	patch_83_84_b.sql|xref.version_default
 127	\N	patch	patch_83_84_c.sql|protein_feature_unique
 128	\N	patch	patch_83_84_d.sql|longer_synonym
+129	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/nameless/core/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index ebd656a1de..462b632269 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -21,18 +21,18 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
@@ -41,7 +41,7 @@ CREATE TABLE `analysis` (
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -99,8 +99,8 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
@@ -151,7 +151,7 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,7 +236,7 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -300,11 +300,11 @@ CREATE TABLE `gene` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=130 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,9 +500,9 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
@@ -511,9 +511,9 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -656,9 +656,9 @@ CREATE TABLE `protein_feature` (
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
@@ -686,7 +686,7 @@ CREATE TABLE `repeat_feature` (
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
@@ -697,7 +697,7 @@ CREATE TABLE `seq_region` (
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -725,7 +725,7 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
@@ -735,12 +735,12 @@ CREATE TABLE `simple_feature` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -786,7 +786,7 @@ CREATE TABLE `transcript` (
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,7 +817,7 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
@@ -828,7 +828,7 @@ CREATE TABLE `translation` (
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,20 +854,20 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
diff --git a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
index 93a00d9664..80008c3ebc 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:19:28 2015
+-- Created on Fri May  6 15:45:55 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -201,7 +201,8 @@ CREATE TABLE closure (
   parent_term_id integer NOT NULL,
   subparent_term_id integer,
   distance tinyint NOT NULL,
-  ontology_id integer NOT NULL
+  ontology_id integer NOT NULL,
+  confident_relationship tinyint NOT NULL
 );
 
 CREATE UNIQUE INDEX child_parent_idx ON closure (child_term_id, parent_term_id, subparent_term_id, ontology_id);
@@ -271,7 +272,8 @@ CREATE TABLE synonym (
   synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   term_id integer NOT NULL,
   name text NOT NULL,
-  type enum
+  type enum,
+  dbxref varchar(64)
 );
 
 CREATE UNIQUE INDEX term_synonym_idx ON synonym (term_id, synonym_id);
diff --git a/modules/t/test-genome-DBs/ontology/ontology/closure.txt b/modules/t/test-genome-DBs/ontology/ontology/closure.txt
index 98123d8bff..10561511aa 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/closure.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/closure.txt
@@ -1,1764 +1,1764 @@
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+1195301	21252	2689	705	7	3	0
+1413199	21252	2688	3916	10	3	0
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+1212078	29619	2688	3916	7	3	0
+1212830	29960	2688	3916	7	3	0
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+1296814	259	2688	2735	8	3	0
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diff --git a/modules/t/test-genome-DBs/ontology/ontology/meta.txt b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
index 0561e40cab..5df37bd58e 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/meta.txt
+++ b/modules/t/test-genome-DBs/ontology/ontology/meta.txt
@@ -20,3 +20,5 @@
 23	patch	patch_81_82_a.sql|schema_version	\N
 24	patch	patch_82_83_a.sql|schema_version	\N
 25	patch	patch_83_84_a.sql|schema_version	\N
+26	patch	patch_84_85_b.sql|confident_relationship	\N
+27	patch	patch_84_85_c.sql| add synonym dbxref	\N
diff --git a/modules/t/test-genome-DBs/ontology/ontology/table.sql b/modules/t/test-genome-DBs/ontology/ontology/table.sql
index 215ce11618..19e329d04f 100644
--- a/modules/t/test-genome-DBs/ontology/ontology/table.sql
+++ b/modules/t/test-genome-DBs/ontology/ontology/table.sql
@@ -126,6 +126,7 @@ CREATE TABLE `closure` (
   `subparent_term_id` int(10) unsigned DEFAULT NULL,
   `distance` tinyint(3) unsigned NOT NULL,
   `ontology_id` int(10) unsigned NOT NULL,
+  `confident_relationship` tinyint(1) NOT NULL,
   PRIMARY KEY (`closure_id`),
   UNIQUE KEY `child_parent_idx` (`child_term_id`,`parent_term_id`,`subparent_term_id`,`ontology_id`),
   KEY `parent_subparent_idx` (`parent_term_id`,`subparent_term_id`)
@@ -138,7 +139,7 @@ CREATE TABLE `meta` (
   `species_id` int(1) unsigned DEFAULT NULL,
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `key_value_idx` (`meta_key`,`meta_value`)
-) ENGINE=MyISAM AUTO_INCREMENT=26 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=28 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `ontology` (
   `ontology_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -180,6 +181,7 @@ CREATE TABLE `synonym` (
   `term_id` int(10) unsigned NOT NULL,
   `name` text NOT NULL,
   `type` enum('EXACT','BROAD','NARROW','RELATED') DEFAULT NULL,
+  `dbxref` varchar(64) DEFAULT NULL,
   PRIMARY KEY (`synonym_id`),
   UNIQUE KEY `term_synonym_idx` (`term_id`,`synonym_id`),
   KEY `name_idx` (`name`(50))
diff --git a/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
index 04acff9412..d6564ea744 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:19:38 2015
+-- Created on Fri May  6 15:46:11 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float(8,2) NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL,
-  type varchar(30) NOT NULL,
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,11 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -303,14 +301,12 @@ CREATE TABLE external_db (
   description text
 );
 
-CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
-
 --
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -380,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -396,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -418,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -437,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -471,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -484,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -496,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -510,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -522,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -531,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -577,24 +573,24 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
@@ -605,7 +601,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -619,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -637,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -664,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -680,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -693,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -714,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision(8,2),
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -735,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -746,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -762,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -796,7 +792,7 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
 CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
@@ -806,12 +802,12 @@ CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -824,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -860,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -911,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -933,7 +929,7 @@ CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, a
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -944,8 +940,6 @@ CREATE TABLE unmapped_object (
   parent varchar(255)
 );
 
-CREATE UNIQUE INDEX unique_unmapped_obj_idx ON unmapped_object (ensembl_id, ensembl_object_type, identifier, unmapped_reason_id, parent, external_db_id);
-
 --
 -- Table: unmapped_reason
 --
diff --git a/modules/t/test-genome-DBs/polyploidy/core/meta.txt b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
index a712f78a80..5877a7bd3a 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/meta.txt
+++ b/modules/t/test-genome-DBs/polyploidy/core/meta.txt
@@ -127,3 +127,4 @@
 207	\N	patch	patch_83_84_b.sql|xref.version_default
 208	\N	patch	patch_83_84_c.sql|protein_feature_unique
 209	\N	patch	patch_83_84_d.sql|longer_synonym
+210	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/polyploidy/core/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index ebd656a1de..0b0a206c97 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -21,27 +21,27 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=201 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -99,12 +99,12 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=437 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
   `coord_system_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -117,7 +117,7 @@ CREATE TABLE `coord_system` (
   UNIQUE KEY `rank_idx` (`rank`,`species_id`),
   UNIQUE KEY `name_idx` (`name`,`version`,`species_id`),
   KEY `species_idx` (`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `data_file` (
   `data_file_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -151,10 +151,10 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=23 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,13 +236,13 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=382467 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -297,14 +297,14 @@ CREATE TABLE `gene` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=40234 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -332,7 +332,7 @@ CREATE TABLE `genome_statistics` (
   PRIMARY KEY (`genome_statistics_id`),
   UNIQUE KEY `stats_uniq` (`statistic`,`attrib_type_id`,`species_id`),
   KEY `stats_idx` (`statistic`,`attrib_type_id`,`species_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `identity_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=211 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,20 +500,20 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=24 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -652,20 +652,20 @@ CREATE TABLE `protein_feature` (
   KEY `translation_id` (`translation_id`),
   KEY `hitname_index` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3502933 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
   KEY `class` (`repeat_class`),
   KEY `consensus` (`repeat_consensus`(10)),
   KEY `type` (`repeat_type`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=1163919 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_feature` (
   `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,22 +682,22 @@ CREATE TABLE `repeat_feature` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `repeat_idx` (`repeat_consensus_id`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM AUTO_INCREMENT=10446798 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
   UNIQUE KEY `coord_system_id` (`coord_system_id`,`name`),
   KEY `name_idx` (`name`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=3495795 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -725,7 +725,7 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
@@ -735,12 +735,12 @@ CREATE TABLE `simple_feature` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -781,12 +781,12 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,18 +817,18 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,20 +854,20 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
diff --git a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
index b81c1ab821..2430ff36ca 100644
--- a/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
@@ -1,6 +1,6 @@
 -- 
 -- Created by SQL::Translator::Producer::SQLite
--- Created on Fri Dec 11 17:19:50 2015
+-- Created on Fri May  6 15:46:27 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -37,7 +37,7 @@ CREATE TABLE alt_allele_group (
 CREATE TABLE analysis (
   analysis_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   created datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  logic_name varchar(128) NOT NULL,
+  logic_name varchar(40) NOT NULL DEFAULT '',
   db varchar(120),
   db_version varchar(40),
   db_file varchar(120),
@@ -51,32 +51,30 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
 
 --
 -- Table: analysis_description
 --
 CREATE TABLE analysis_description (
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL DEFAULT 0,
   description text,
-  display_label varchar(255) NOT NULL,
+  display_label varchar(255),
   displayable tinyint NOT NULL DEFAULT 1,
   web_data text
 );
 
-CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
-
 --
 -- Table: assembly
 --
 CREATE TABLE assembly (
-  asm_seq_region_id integer NOT NULL,
-  cmp_seq_region_id integer NOT NULL,
-  asm_start integer NOT NULL,
-  asm_end integer NOT NULL,
-  cmp_start integer NOT NULL,
-  cmp_end integer NOT NULL,
-  ori tinyint NOT NULL
+  asm_seq_region_id integer NOT NULL DEFAULT 0,
+  cmp_seq_region_id integer NOT NULL DEFAULT 0,
+  asm_start integer NOT NULL DEFAULT 0,
+  asm_end integer NOT NULL DEFAULT 0,
+  cmp_start integer NOT NULL DEFAULT 0,
+  cmp_end integer NOT NULL DEFAULT 0,
+  ori tinyint NOT NULL DEFAULT 0
 );
 
 CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, asm_start, asm_end, cmp_start, cmp_end, ori);
@@ -86,14 +84,14 @@ CREATE UNIQUE INDEX all_idx ON assembly (asm_seq_region_id, cmp_seq_region_id, a
 --
 CREATE TABLE assembly_exception (
   assembly_exception_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  exc_type enum NOT NULL,
-  exc_seq_region_id integer NOT NULL,
-  exc_seq_region_start integer NOT NULL,
-  exc_seq_region_end integer NOT NULL,
-  ori integer NOT NULL
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  exc_type enum NOT NULL DEFAULT 'HAP',
+  exc_seq_region_id integer NOT NULL DEFAULT 0,
+  exc_seq_region_start integer NOT NULL DEFAULT 0,
+  exc_seq_region_end integer NOT NULL DEFAULT 0,
+  ori integer NOT NULL DEFAULT 0
 );
 
 --
@@ -129,7 +127,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX code_idx ON attrib_type (code);
+CREATE UNIQUE INDEX c ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -168,11 +166,11 @@ CREATE UNIQUE INDEX df_unq_idx ON data_file (coord_system_id, analysis_id, name,
 --
 CREATE TABLE density_feature (
   density_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  density_type_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  density_value float NOT NULL
+  density_type_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  density_value float NOT NULL DEFAULT 0
 );
 
 --
@@ -180,13 +178,13 @@ CREATE TABLE density_feature (
 --
 CREATE TABLE density_type (
   density_type_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  analysis_id smallint NOT NULL,
-  block_size integer NOT NULL,
-  region_features integer NOT NULL,
-  value_type enum NOT NULL
+  analysis_id integer NOT NULL DEFAULT 0,
+  block_size integer NOT NULL DEFAULT 0,
+  region_features integer NOT NULL DEFAULT 0,
+  value_type enum NOT NULL DEFAULT 'sum'
 );
 
-CREATE UNIQUE INDEX analysis_idx02 ON density_type (analysis_id, block_size, region_features);
+CREATE UNIQUE INDEX analysis_id ON density_type (analysis_id, block_size, region_features);
 
 --
 -- Table: dependent_xref
@@ -202,10 +200,10 @@ CREATE TABLE dependent_xref (
 --
 CREATE TABLE ditag (
   ditag_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(30) NOT NULL,
-  type varchar(30) NOT NULL,
-  tag_count smallint NOT NULL DEFAULT 1,
-  sequence tinytext NOT NULL
+  name varchar(30),
+  type varchar(30),
+  tag_count smallint DEFAULT 1,
+  sequence text
 );
 
 --
@@ -219,20 +217,20 @@ CREATE TABLE ditag_feature (
   seq_region_start integer NOT NULL DEFAULT 0,
   seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 0,
-  analysis_id smallint NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   hit_start integer NOT NULL DEFAULT 0,
   hit_end integer NOT NULL DEFAULT 0,
   hit_strand tinyint NOT NULL DEFAULT 0,
-  cigar_line tinytext NOT NULL,
-  ditag_side enum NOT NULL
+  cigar_line text,
+  ditag_side char(1) DEFAULT ''
 );
 
 --
 -- Table: dna
 --
 CREATE TABLE dna (
-  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  sequence longtext NOT NULL
+  seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  sequence mediumtext NOT NULL
 );
 
 --
@@ -240,20 +238,20 @@ CREATE TABLE dna (
 --
 CREATE TABLE dna_align_feature (
   dna_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_strand tinyint NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_strand tinyint NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision,
   external_data text
 );
@@ -272,7 +270,7 @@ CREATE TABLE exon (
   is_current tinyint NOT NULL DEFAULT 1,
   is_constitutive tinyint NOT NULL DEFAULT 0,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -281,9 +279,9 @@ CREATE TABLE exon (
 -- Table: exon_transcript
 --
 CREATE TABLE exon_transcript (
-  exon_id integer NOT NULL,
-  transcript_id integer NOT NULL,
-  rank integer NOT NULL,
+  exon_id integer NOT NULL DEFAULT 0,
+  transcript_id integer NOT NULL DEFAULT 0,
+  rank integer NOT NULL DEFAULT 0,
   PRIMARY KEY (exon_id, transcript_id, rank)
 );
 
@@ -291,11 +289,11 @@ CREATE TABLE exon_transcript (
 -- Table: external_db
 --
 CREATE TABLE external_db (
-  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  db_name varchar(100) NOT NULL,
-  db_release varchar(255),
-  status enum NOT NULL,
-  priority integer NOT NULL,
+  external_db_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
+  db_name varchar(27) NOT NULL DEFAULT '',
+  db_release varchar(40) NOT NULL DEFAULT '',
+  status enum NOT NULL DEFAULT 'KNOWNXREF',
+  priority integer NOT NULL DEFAULT 0,
   db_display_name varchar(255),
   type enum,
   secondary_db_name varchar(255),
@@ -303,14 +301,12 @@ CREATE TABLE external_db (
   description text
 );
 
-CREATE UNIQUE INDEX db_name_idx ON external_db (db_name, db_release);
-
 --
 -- Table: external_synonym
 --
 CREATE TABLE external_synonym (
-  xref_id integer NOT NULL,
-  synonym varchar(100) NOT NULL,
+  xref_id integer NOT NULL DEFAULT 0,
+  synonym varchar(40) NOT NULL DEFAULT '',
   PRIMARY KEY (xref_id, synonym)
 );
 
@@ -332,7 +328,7 @@ CREATE TABLE gene (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_transcript_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -341,14 +337,14 @@ CREATE TABLE gene (
 -- Table: gene_archive
 --
 CREATE TABLE gene_archive (
-  gene_stable_id varchar(128) NOT NULL,
-  gene_version smallint NOT NULL DEFAULT 1,
-  transcript_stable_id varchar(128) NOT NULL,
-  transcript_version smallint NOT NULL DEFAULT 1,
-  translation_stable_id varchar(128),
-  translation_version smallint NOT NULL DEFAULT 1,
-  peptide_archive_id integer,
-  mapping_session_id integer NOT NULL
+  gene_stable_id varchar(128) NOT NULL DEFAULT '',
+  gene_version smallint NOT NULL DEFAULT 0,
+  transcript_stable_id varchar(128) NOT NULL DEFAULT '',
+  transcript_version smallint NOT NULL DEFAULT 0,
+  translation_stable_id varchar(128) NOT NULL DEFAULT '',
+  translation_version smallint NOT NULL DEFAULT 0,
+  peptide_archive_id integer NOT NULL DEFAULT 0,
+  mapping_session_id integer NOT NULL DEFAULT 0
 );
 
 --
@@ -380,7 +376,7 @@ CREATE UNIQUE INDEX stats_uniq ON genome_statistics (statistic, attrib_type_id,
 -- Table: identity_xref
 --
 CREATE TABLE identity_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL DEFAULT 0,
   xref_identity integer,
   ensembl_identity integer,
   xref_start integer,
@@ -396,11 +392,11 @@ CREATE TABLE identity_xref (
 -- Table: interpro
 --
 CREATE TABLE interpro (
-  interpro_ac varchar(40) NOT NULL,
-  id varchar(40) NOT NULL
+  interpro_ac varchar(40) NOT NULL DEFAULT '',
+  id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -418,16 +414,16 @@ CREATE TABLE intron_supporting_evidence (
   is_splice_canonical tinyint NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX analysis_id ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
+CREATE UNIQUE INDEX analysis_id02 ON intron_supporting_evidence (analysis_id, seq_region_id, seq_region_start, seq_region_end, seq_region_strand, hit_name);
 
 --
 -- Table: karyotype
 --
 CREATE TABLE karyotype (
   karyotype_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   band varchar(40),
   stain varchar(40)
 );
@@ -437,7 +433,7 @@ CREATE TABLE karyotype (
 --
 CREATE TABLE map (
   map_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  map_name varchar(30) NOT NULL
+  map_name varchar(30) NOT NULL DEFAULT ''
 );
 
 --
@@ -451,8 +447,7 @@ CREATE TABLE mapping_session (
   new_release varchar(5) NOT NULL DEFAULT '',
   old_assembly varchar(20) NOT NULL DEFAULT '',
   new_assembly varchar(20) NOT NULL DEFAULT '',
-  created datetime NOT NULL,
-  species_id integer NOT NULL
+  created datetime NOT NULL
 );
 
 --
@@ -472,10 +467,10 @@ CREATE UNIQUE INDEX mapping_idx ON mapping_set (internal_schema_build, external_
 CREATE TABLE marker (
   marker_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   display_marker_synonym_id integer,
-  left_primer varchar(100) NOT NULL,
-  right_primer varchar(100) NOT NULL,
-  min_primer_dist integer NOT NULL,
-  max_primer_dist integer NOT NULL,
+  left_primer varchar(100) NOT NULL DEFAULT '',
+  right_primer varchar(100) NOT NULL DEFAULT '',
+  min_primer_dist integer NOT NULL DEFAULT 0,
+  max_primer_dist integer NOT NULL DEFAULT 0,
   priority integer,
   type enum
 );
@@ -485,11 +480,11 @@ CREATE TABLE marker (
 --
 CREATE TABLE marker_feature (
   marker_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   map_weight integer
 );
 
@@ -497,11 +492,11 @@ CREATE TABLE marker_feature (
 -- Table: marker_map_location
 --
 CREATE TABLE marker_map_location (
-  marker_id integer NOT NULL,
-  map_id integer NOT NULL,
-  chromosome_name varchar(15) NOT NULL,
-  marker_synonym_id integer NOT NULL,
-  position varchar(15) NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
+  map_id integer NOT NULL DEFAULT 0,
+  chromosome_name varchar(15) NOT NULL DEFAULT '',
+  marker_synonym_id integer NOT NULL DEFAULT 0,
+  position varchar(15) NOT NULL DEFAULT '',
   lod_score double precision,
   PRIMARY KEY (marker_id, map_id)
 );
@@ -511,9 +506,9 @@ CREATE TABLE marker_map_location (
 --
 CREATE TABLE marker_synonym (
   marker_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  marker_id integer NOT NULL,
+  marker_id integer NOT NULL DEFAULT 0,
   source varchar(20),
-  name varchar(50)
+  name varchar(30)
 );
 
 --
@@ -523,7 +518,7 @@ CREATE TABLE meta (
   meta_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   species_id integer DEFAULT 1,
   meta_key varchar(40) NOT NULL,
-  meta_value varchar(255)
+  meta_value varchar(255) NOT NULL
 );
 
 CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_value);
@@ -532,12 +527,12 @@ CREATE UNIQUE INDEX species_key_value_idx ON meta (species_id, meta_key, meta_va
 -- Table: meta_coord
 --
 CREATE TABLE meta_coord (
-  table_name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
+  table_name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
   max_length integer
 );
 
-CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
+CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
 
 --
 -- Table: misc_attrib
@@ -578,35 +573,35 @@ CREATE TABLE misc_set (
   code varchar(25) NOT NULL DEFAULT '',
   name varchar(255) NOT NULL DEFAULT '',
   description text NOT NULL,
-  max_length integer NOT NULL
+  max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
+CREATE UNIQUE INDEX c02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  ensembl_id integer NOT NULL,
-  ensembl_object_type enum NOT NULL,
+  object_xref_id integer NOT NULL,
+  ensembl_id integer NOT NULL DEFAULT 0,
+  ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
   linkage_annotation varchar(255),
-  analysis_id smallint NOT NULL DEFAULT 0
+  analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
+CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
 
 --
 -- Table: ontology_xref
 --
 CREATE TABLE ontology_xref (
   object_xref_id integer NOT NULL DEFAULT 0,
-  source_xref_id integer,
-  linkage_type varchar(3)
+  linkage_type varchar(3),
+  source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -620,7 +615,7 @@ CREATE TABLE operon (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -638,7 +633,7 @@ CREATE TABLE operon_transcript (
   display_label varchar(255),
   analysis_id smallint NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -665,13 +660,13 @@ CREATE TABLE peptide_archive (
 --
 CREATE TABLE prediction_exon (
   prediction_exon_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  prediction_transcript_id integer NOT NULL,
-  exon_rank smallint NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  start_phase tinyint NOT NULL,
+  prediction_transcript_id integer NOT NULL DEFAULT 0,
+  exon_rank smallint NOT NULL DEFAULT 0,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  start_phase tinyint NOT NULL DEFAULT 0,
   score double precision,
   p_value double precision
 );
@@ -681,11 +676,11 @@ CREATE TABLE prediction_exon (
 --
 CREATE TABLE prediction_transcript (
   prediction_transcript_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  analysis_id integer,
   display_label varchar(255)
 );
 
@@ -694,19 +689,19 @@ CREATE TABLE prediction_transcript (
 --
 CREATE TABLE protein_align_feature (
   protein_align_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision,
   evalue double precision,
   perc_ident float,
   cigar_line text,
-  external_db_id integer,
+  external_db_id smallint,
   hcoverage double precision
 );
 
@@ -715,14 +710,14 @@ CREATE TABLE protein_align_feature (
 --
 CREATE TABLE protein_feature (
   protein_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  translation_id integer NOT NULL,
-  seq_start integer NOT NULL,
-  seq_end integer NOT NULL,
-  hit_start integer NOT NULL,
-  hit_end integer NOT NULL,
-  hit_name varchar(40) NOT NULL,
-  analysis_id smallint NOT NULL,
-  score double precision,
+  translation_id integer NOT NULL DEFAULT 0,
+  seq_start integer NOT NULL DEFAULT 0,
+  seq_end integer NOT NULL DEFAULT 0,
+  hit_start integer NOT NULL DEFAULT 0,
+  hit_end integer NOT NULL DEFAULT 0,
+  hit_name varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
+  score double precision NOT NULL DEFAULT 0,
   evalue double precision,
   perc_ident float,
   external_data text,
@@ -736,9 +731,9 @@ CREATE UNIQUE INDEX aln_idx ON protein_feature (translation_id, hit_name, seq_st
 --
 CREATE TABLE repeat_consensus (
   repeat_consensus_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  repeat_name varchar(255) NOT NULL,
-  repeat_class varchar(100) NOT NULL,
-  repeat_type varchar(40) NOT NULL,
+  repeat_name varchar(255) NOT NULL DEFAULT '',
+  repeat_class varchar(100) NOT NULL DEFAULT '',
+  repeat_type varchar(40) NOT NULL DEFAULT '',
   repeat_consensus text
 );
 
@@ -747,14 +742,14 @@ CREATE TABLE repeat_consensus (
 --
 CREATE TABLE repeat_feature (
   repeat_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
   seq_region_strand tinyint NOT NULL DEFAULT 1,
-  repeat_start integer NOT NULL,
-  repeat_end integer NOT NULL,
-  repeat_consensus_id integer NOT NULL,
-  analysis_id smallint NOT NULL,
+  repeat_start integer NOT NULL DEFAULT 0,
+  repeat_end integer NOT NULL DEFAULT 0,
+  repeat_consensus_id integer NOT NULL DEFAULT 0,
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -763,12 +758,12 @@ CREATE TABLE repeat_feature (
 --
 CREATE TABLE seq_region (
   seq_region_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  name varchar(40) NOT NULL,
-  coord_system_id integer NOT NULL,
-  length integer NOT NULL
+  name varchar(40) NOT NULL DEFAULT '',
+  coord_system_id integer NOT NULL DEFAULT 0,
+  length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
+CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
 
 --
 -- Table: seq_region_attrib
@@ -797,7 +792,7 @@ CREATE TABLE seq_region_synonym (
   seq_region_synonym_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   seq_region_id integer NOT NULL,
   synonym varchar(250) NOT NULL,
-  external_db_id integer
+  external_db_id smallint
 );
 
 CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
@@ -807,12 +802,12 @@ CREATE UNIQUE INDEX syn_idx ON seq_region_synonym (synonym, seq_region_id);
 --
 CREATE TABLE simple_feature (
   simple_feature_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
-  seq_region_id integer NOT NULL,
-  seq_region_start integer NOT NULL,
-  seq_region_end integer NOT NULL,
-  seq_region_strand tinyint NOT NULL,
-  display_label varchar(255) NOT NULL,
-  analysis_id smallint NOT NULL,
+  seq_region_id integer NOT NULL DEFAULT 0,
+  seq_region_start integer NOT NULL DEFAULT 0,
+  seq_region_end integer NOT NULL DEFAULT 0,
+  seq_region_strand tinyint NOT NULL DEFAULT 0,
+  display_label varchar(40) NOT NULL DEFAULT '',
+  analysis_id integer NOT NULL DEFAULT 0,
   score double precision
 );
 
@@ -825,11 +820,11 @@ CREATE TABLE stable_id_event (
   new_stable_id varchar(128),
   new_version smallint,
   mapping_session_id integer NOT NULL DEFAULT 0,
-  type enum NOT NULL,
+  type enum NOT NULL DEFAULT 'gene',
   score float NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, new_stable_id, type);
+CREATE UNIQUE INDEX uni_idx ON stable_id_event (mapping_session_id, old_stable_id, old_version, new_stable_id, new_version, type);
 
 --
 -- Table: supporting_feature
@@ -861,7 +856,7 @@ CREATE TABLE transcript (
   is_current tinyint NOT NULL DEFAULT 1,
   canonical_translation_id integer,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -912,7 +907,7 @@ CREATE TABLE translation (
   seq_end integer NOT NULL,
   end_exon_id integer NOT NULL,
   stable_id varchar(128),
-  version smallint NOT NULL DEFAULT 1,
+  version smallint,
   created_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   modified_date datetime NOT NULL DEFAULT '0000-00-00 00:00:00'
 );
@@ -934,7 +929,7 @@ CREATE UNIQUE INDEX translation_attribx ON translation_attrib (translation_id, a
 CREATE TABLE unmapped_object (
   unmapped_object_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   type enum NOT NULL,
-  analysis_id smallint NOT NULL,
+  analysis_id integer NOT NULL,
   external_db_id integer,
   identifier varchar(255) NOT NULL,
   unmapped_reason_id integer NOT NULL,
@@ -945,8 +940,6 @@ CREATE TABLE unmapped_object (
   parent varchar(255)
 );
 
-CREATE UNIQUE INDEX unique_unmapped_obj_idx ON unmapped_object (ensembl_id, ensembl_object_type, identifier, unmapped_reason_id, parent, external_db_id);
-
 --
 -- Table: unmapped_reason
 --
diff --git a/modules/t/test-genome-DBs/test_collection/core/meta.txt b/modules/t/test-genome-DBs/test_collection/core/meta.txt
index 282eb0419c..f6fbef56a1 100644
--- a/modules/t/test-genome-DBs/test_collection/core/meta.txt
+++ b/modules/t/test-genome-DBs/test_collection/core/meta.txt
@@ -147,3 +147,4 @@
 140	2	species.taxonomy_id	1217737
 131	2	species.url	Bacillus_thuringiensis_hd_790
 155	2	transcriptbuild.level	toplevel
+192	\N	patch	patch_83_84_e.sql|nullable_versions
diff --git a/modules/t/test-genome-DBs/test_collection/core/table.sql b/modules/t/test-genome-DBs/test_collection/core/table.sql
index ebd656a1de..9150552e0a 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -21,18 +21,18 @@ CREATE TABLE `alt_allele_group` (
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `created` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
-  `logic_name` varchar(40) NOT NULL DEFAULT '',
-  `db` varchar(120) DEFAULT NULL,
-  `db_version` varchar(40) DEFAULT NULL,
-  `db_file` varchar(120) DEFAULT NULL,
-  `program` varchar(80) DEFAULT NULL,
-  `program_version` varchar(40) DEFAULT NULL,
-  `program_file` varchar(80) DEFAULT NULL,
+  `logic_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `db_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `db_file` varchar(120) COLLATE latin1_bin DEFAULT NULL,
+  `program` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `program_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `program_file` varchar(80) COLLATE latin1_bin DEFAULT NULL,
   `parameters` text COLLATE latin1_bin,
-  `module` varchar(80) DEFAULT NULL,
-  `module_version` varchar(40) DEFAULT NULL,
-  `gff_source` varchar(40) DEFAULT NULL,
-  `gff_feature` varchar(40) DEFAULT NULL,
+  `module` varchar(80) COLLATE latin1_bin DEFAULT NULL,
+  `module_version` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_source` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `gff_feature` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`analysis_id`),
   UNIQUE KEY `logic_name` (`logic_name`),
   KEY `logic_name_idx` (`logic_name`)
@@ -41,7 +41,7 @@ CREATE TABLE `analysis` (
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `description` text COLLATE latin1_bin,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `displayable` tinyint(1) NOT NULL DEFAULT '1',
   `web_data` text COLLATE latin1_bin,
   KEY `analysis_idx` (`analysis_id`)
@@ -65,7 +65,7 @@ CREATE TABLE `assembly_exception` (
   `seq_region_id` int(11) NOT NULL DEFAULT '0',
   `seq_region_start` int(11) NOT NULL DEFAULT '0',
   `seq_region_end` int(11) NOT NULL DEFAULT '0',
-  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') NOT NULL DEFAULT 'HAP',
+  `exc_type` enum('HAP','PAR','PATCH_NOVEL','PATCH_FIX') COLLATE latin1_bin NOT NULL DEFAULT 'HAP',
   `exc_seq_region_id` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_start` int(11) NOT NULL DEFAULT '0',
   `exc_seq_region_end` int(11) NOT NULL DEFAULT '0',
@@ -99,8 +99,8 @@ CREATE TABLE `associated_xref` (
 
 CREATE TABLE `attrib_type` (
   `attrib_type_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(20) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
+  `code` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
   UNIQUE KEY `c` (`code`)
@@ -151,7 +151,7 @@ CREATE TABLE `density_type` (
   `analysis_id` int(11) NOT NULL DEFAULT '0',
   `block_size` int(11) NOT NULL DEFAULT '0',
   `region_features` int(11) NOT NULL DEFAULT '0',
-  `value_type` enum('sum','ratio') NOT NULL DEFAULT 'sum',
+  `value_type` enum('sum','ratio') COLLATE latin1_bin NOT NULL DEFAULT 'sum',
   PRIMARY KEY (`density_type_id`),
   UNIQUE KEY `analysis_id` (`analysis_id`,`block_size`,`region_features`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -195,7 +195,7 @@ CREATE TABLE `ditag_feature` (
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `sequence` mediumtext NOT NULL,
+  `sequence` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=750000 AVG_ROW_LENGTH=19000;
 
@@ -208,7 +208,7 @@ CREATE TABLE `dna_align_feature` (
   `hit_start` int(11) NOT NULL DEFAULT '0',
   `hit_end` int(11) NOT NULL DEFAULT '0',
   `hit_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -236,7 +236,7 @@ CREATE TABLE `exon` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `is_constitutive` tinyint(1) NOT NULL DEFAULT '0',
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`exon_id`),
@@ -255,21 +255,21 @@ CREATE TABLE `exon_transcript` (
 
 CREATE TABLE `external_db` (
   `external_db_id` int(11) NOT NULL DEFAULT '0',
-  `db_name` varchar(27) NOT NULL DEFAULT '',
-  `db_release` varchar(40) NOT NULL DEFAULT '',
-  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') NOT NULL DEFAULT 'KNOWNXREF',
+  `db_name` varchar(27) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `db_release` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `status` enum('KNOWNXREF','KNOWN','XREF','PRED','ORTH','PSEUDO') COLLATE latin1_bin NOT NULL DEFAULT 'KNOWNXREF',
   `priority` int(11) NOT NULL DEFAULT '0',
-  `db_display_name` varchar(255) DEFAULT NULL,
-  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') DEFAULT NULL,
-  `secondary_db_name` varchar(255) DEFAULT NULL,
-  `secondary_db_table` varchar(255) DEFAULT NULL,
+  `db_display_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `type` enum('ARRAY','ALT_TRANS','ALT_GENE','MISC','LIT','PRIMARY_DB_SYNONYM','ENSEMBL') COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_name` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `secondary_db_table` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
   `xref_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `synonym` varchar(40) NOT NULL DEFAULT '',
+  `synonym` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`,`synonym`),
   KEY `name_index` (`synonym`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -289,7 +289,7 @@ CREATE TABLE `gene` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`gene_id`),
@@ -300,11 +300,11 @@ CREATE TABLE `gene` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
-  `gene_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `gene_version` smallint(6) NOT NULL DEFAULT '0',
-  `transcript_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `transcript_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `transcript_version` smallint(6) NOT NULL DEFAULT '0',
-  `translation_stable_id` varchar(128) NOT NULL DEFAULT '',
+  `translation_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
   `translation_version` smallint(6) NOT NULL DEFAULT '0',
   `peptide_archive_id` int(11) NOT NULL DEFAULT '0',
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
@@ -316,7 +316,7 @@ CREATE TABLE `gene_archive` (
 CREATE TABLE `gene_attrib` (
   `gene_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `gene_attribx` (`gene_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `gene_idx` (`gene_id`)
@@ -349,8 +349,8 @@ CREATE TABLE `identity_xref` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `interpro` (
-  `interpro_ac` varchar(40) NOT NULL DEFAULT '',
-  `id` varchar(40) NOT NULL DEFAULT '',
+  `interpro_ac` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `id` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   UNIQUE KEY `interpro_ac` (`interpro_ac`,`id`),
   KEY `id` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -376,26 +376,26 @@ CREATE TABLE `karyotype` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_start` int(10) NOT NULL DEFAULT '0',
   `seq_region_end` int(10) NOT NULL DEFAULT '0',
-  `band` varchar(40) DEFAULT NULL,
-  `stain` varchar(40) DEFAULT NULL,
+  `band` varchar(40) COLLATE latin1_bin DEFAULT NULL,
+  `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `map_name` varchar(30) NOT NULL DEFAULT '',
+  `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
-  `old_db_name` varchar(80) NOT NULL DEFAULT '',
-  `new_db_name` varchar(80) NOT NULL DEFAULT '',
-  `old_release` varchar(5) NOT NULL DEFAULT '',
-  `new_release` varchar(5) NOT NULL DEFAULT '',
-  `old_assembly` varchar(20) NOT NULL DEFAULT '',
-  `new_assembly` varchar(20) NOT NULL DEFAULT '',
+  `old_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_db_name` varchar(80) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_release` varchar(5) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `old_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -411,12 +411,12 @@ CREATE TABLE `mapping_set` (
 CREATE TABLE `marker` (
   `marker_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `display_marker_synonym_id` int(10) unsigned DEFAULT NULL,
-  `left_primer` varchar(100) NOT NULL DEFAULT '',
-  `right_primer` varchar(100) NOT NULL DEFAULT '',
+  `left_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `right_primer` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
   `min_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `max_primer_dist` int(10) unsigned NOT NULL DEFAULT '0',
   `priority` int(11) DEFAULT NULL,
-  `type` enum('est','microsatellite') DEFAULT NULL,
+  `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
   KEY `marker_idx` (`marker_id`,`priority`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -437,9 +437,9 @@ CREATE TABLE `marker_feature` (
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
   `map_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `chromosome_name` varchar(15) NOT NULL DEFAULT '',
+  `chromosome_name` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `marker_synonym_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `position` varchar(15) NOT NULL DEFAULT '',
+  `position` varchar(15) COLLATE latin1_bin NOT NULL DEFAULT '',
   `lod_score` double DEFAULT NULL,
   PRIMARY KEY (`marker_id`,`map_id`),
   KEY `map_idx` (`map_id`,`chromosome_name`,`position`)
@@ -448,8 +448,8 @@ CREATE TABLE `marker_map_location` (
 CREATE TABLE `marker_synonym` (
   `marker_synonym_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `source` varchar(20) DEFAULT NULL,
-  `name` varchar(30) DEFAULT NULL,
+  `source` varchar(20) COLLATE latin1_bin DEFAULT NULL,
+  `name` varchar(30) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
@@ -463,10 +463,10 @@ CREATE TABLE `meta` (
   PRIMARY KEY (`meta_id`),
   UNIQUE KEY `species_key_value_idx` (`species_id`,`meta_key`,`meta_value`),
   KEY `species_value_idx` (`species_id`,`meta_value`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=193 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
-  `table_name` varchar(40) NOT NULL DEFAULT '',
+  `table_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(11) NOT NULL DEFAULT '0',
   `max_length` int(11) DEFAULT NULL,
   UNIQUE KEY `table_name` (`table_name`,`coord_system_id`)
@@ -475,7 +475,7 @@ CREATE TABLE `meta_coord` (
 CREATE TABLE `misc_attrib` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `misc_attribx` (`misc_feature_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
@@ -500,9 +500,9 @@ CREATE TABLE `misc_feature_misc_set` (
 
 CREATE TABLE `misc_set` (
   `misc_set_id` smallint(5) unsigned NOT NULL AUTO_INCREMENT,
-  `code` varchar(25) NOT NULL DEFAULT '',
-  `name` varchar(255) NOT NULL DEFAULT '',
-  `description` text NOT NULL,
+  `code` varchar(25) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `description` text COLLATE latin1_bin NOT NULL,
   `max_length` int(10) unsigned NOT NULL DEFAULT '0',
   PRIMARY KEY (`misc_set_id`),
   UNIQUE KEY `c` (`code`)
@@ -511,9 +511,9 @@ CREATE TABLE `misc_set` (
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
   `ensembl_id` int(10) unsigned NOT NULL DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') NOT NULL DEFAULT 'RawContig',
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation','regulatory_factor','regulatory_feature','Marker') COLLATE latin1_bin NOT NULL DEFAULT 'RawContig',
   `xref_id` int(10) unsigned NOT NULL,
-  `linkage_annotation` varchar(255) DEFAULT NULL,
+  `linkage_annotation` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   UNIQUE KEY `ensembl_object_type` (`ensembl_object_type`,`ensembl_id`,`xref_id`),
   KEY `oxref_idx` (`object_xref_id`,`xref_id`,`ensembl_object_type`,`ensembl_id`),
@@ -538,7 +538,7 @@ CREATE TABLE `operon` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_id`),
@@ -557,7 +557,7 @@ CREATE TABLE `operon_transcript` (
   `display_label` varchar(255) DEFAULT NULL,
   `analysis_id` smallint(5) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`operon_transcript_id`),
@@ -574,8 +574,8 @@ CREATE TABLE `operon_transcript_gene` (
 
 CREATE TABLE `peptide_archive` (
   `peptide_archive_id` int(11) NOT NULL AUTO_INCREMENT,
-  `md5_checksum` varchar(32) DEFAULT NULL,
-  `peptide_seq` mediumtext NOT NULL,
+  `md5_checksum` varchar(32) COLLATE latin1_bin DEFAULT NULL,
+  `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
@@ -603,7 +603,7 @@ CREATE TABLE `prediction_transcript` (
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(4) NOT NULL DEFAULT '0',
   `analysis_id` int(11) DEFAULT NULL,
-  `display_label` varchar(255) DEFAULT NULL,
+  `display_label` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`prediction_transcript_id`),
   KEY `seq_region_id` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
@@ -617,7 +617,7 @@ CREATE TABLE `protein_align_feature` (
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '1',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   `evalue` double DEFAULT NULL,
@@ -640,7 +640,7 @@ CREATE TABLE `protein_feature` (
   `seq_end` int(10) NOT NULL DEFAULT '0',
   `hit_start` int(10) NOT NULL DEFAULT '0',
   `hit_end` int(10) NOT NULL DEFAULT '0',
-  `hit_name` varchar(40) NOT NULL DEFAULT '',
+  `hit_name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double NOT NULL DEFAULT '0',
   `evalue` double DEFAULT NULL,
@@ -656,9 +656,9 @@ CREATE TABLE `protein_feature` (
 
 CREATE TABLE `repeat_consensus` (
   `repeat_consensus_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `repeat_name` varchar(255) NOT NULL DEFAULT '',
-  `repeat_class` varchar(100) NOT NULL DEFAULT '',
-  `repeat_type` varchar(40) NOT NULL DEFAULT '',
+  `repeat_name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_class` varchar(100) COLLATE latin1_bin NOT NULL DEFAULT '',
+  `repeat_type` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `repeat_consensus` text COLLATE latin1_bin,
   PRIMARY KEY (`repeat_consensus_id`),
   KEY `name` (`repeat_name`),
@@ -686,7 +686,7 @@ CREATE TABLE `repeat_feature` (
 
 CREATE TABLE `seq_region` (
   `seq_region_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `name` varchar(40) NOT NULL DEFAULT '',
+  `name` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `coord_system_id` int(10) NOT NULL DEFAULT '0',
   `length` int(10) NOT NULL DEFAULT '0',
   PRIMARY KEY (`seq_region_id`),
@@ -697,7 +697,7 @@ CREATE TABLE `seq_region` (
 CREATE TABLE `seq_region_attrib` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `region_attribx` (`seq_region_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
@@ -725,7 +725,7 @@ CREATE TABLE `simple_feature` (
   `seq_region_start` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_end` int(10) unsigned NOT NULL DEFAULT '0',
   `seq_region_strand` tinyint(1) NOT NULL DEFAULT '0',
-  `display_label` varchar(40) NOT NULL DEFAULT '',
+  `display_label` varchar(40) COLLATE latin1_bin NOT NULL DEFAULT '',
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
   `score` double DEFAULT NULL,
   PRIMARY KEY (`simple_feature_id`),
@@ -735,12 +735,12 @@ CREATE TABLE `simple_feature` (
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
 
 CREATE TABLE `stable_id_event` (
-  `old_stable_id` varchar(128) DEFAULT NULL,
+  `old_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `old_version` smallint(6) DEFAULT NULL,
-  `new_stable_id` varchar(128) DEFAULT NULL,
+  `new_stable_id` varchar(128) COLLATE latin1_bin DEFAULT NULL,
   `new_version` smallint(6) DEFAULT NULL,
   `mapping_session_id` int(10) NOT NULL DEFAULT '0',
-  `type` enum('gene','transcript','translation') NOT NULL DEFAULT 'gene',
+  `type` enum('gene','transcript','translation') COLLATE latin1_bin NOT NULL DEFAULT 'gene',
   `score` float NOT NULL DEFAULT '0',
   UNIQUE KEY `uni_idx` (`mapping_session_id`,`old_stable_id`,`old_version`,`new_stable_id`,`new_version`,`type`),
   KEY `new_idx` (`new_stable_id`),
@@ -749,7 +749,7 @@ CREATE TABLE `stable_id_event` (
 
 CREATE TABLE `supporting_feature` (
   `exon_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`exon_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -771,7 +771,7 @@ CREATE TABLE `transcript` (
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`transcript_id`),
@@ -786,7 +786,7 @@ CREATE TABLE `transcript` (
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `transcript_attribx` (`transcript_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
@@ -803,7 +803,7 @@ CREATE TABLE `transcript_intron_supporting_evidence` (
 
 CREATE TABLE `transcript_supporting_feature` (
   `transcript_id` int(11) NOT NULL DEFAULT '0',
-  `feature_type` enum('dna_align_feature','protein_align_feature') DEFAULT NULL,
+  `feature_type` enum('dna_align_feature','protein_align_feature') COLLATE latin1_bin DEFAULT NULL,
   `feature_id` int(11) NOT NULL DEFAULT '0',
   UNIQUE KEY `all_idx` (`transcript_id`,`feature_type`,`feature_id`),
   KEY `feature_idx` (`feature_type`,`feature_id`)
@@ -817,7 +817,7 @@ CREATE TABLE `translation` (
   `seq_end` int(10) NOT NULL,
   `end_exon_id` int(10) unsigned NOT NULL,
   `stable_id` varchar(128) DEFAULT NULL,
-  `version` smallint(5) unsigned NOT NULL DEFAULT '1',
+  `version` smallint(5) unsigned DEFAULT NULL,
   `created_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   `modified_date` datetime NOT NULL DEFAULT '0000-00-00 00:00:00',
   PRIMARY KEY (`translation_id`),
@@ -828,7 +828,7 @@ CREATE TABLE `translation` (
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
   `attrib_type_id` smallint(5) unsigned NOT NULL DEFAULT '0',
-  `value` text NOT NULL,
+  `value` text COLLATE latin1_bin NOT NULL,
   UNIQUE KEY `translation_attribx` (`translation_id`,`attrib_type_id`,`value`(500)),
   KEY `type_val_idx` (`attrib_type_id`,`value`(40)),
   KEY `translation_idx` (`translation_id`)
@@ -836,16 +836,16 @@ CREATE TABLE `translation_attrib` (
 
 CREATE TABLE `unmapped_object` (
   `unmapped_object_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `type` enum('xref','cDNA','Marker') NOT NULL,
+  `type` enum('xref','cDNA','Marker') COLLATE latin1_bin NOT NULL,
   `analysis_id` int(10) unsigned NOT NULL,
   `external_db_id` int(11) DEFAULT NULL,
-  `identifier` varchar(255) NOT NULL,
+  `identifier` varchar(255) COLLATE latin1_bin NOT NULL,
   `unmapped_reason_id` int(10) unsigned NOT NULL,
   `query_score` double DEFAULT NULL,
   `target_score` double DEFAULT NULL,
   `ensembl_id` int(10) unsigned DEFAULT '0',
-  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') DEFAULT 'RawContig',
-  `parent` varchar(255) DEFAULT NULL,
+  `ensembl_object_type` enum('RawContig','Transcript','Gene','Translation') COLLATE latin1_bin DEFAULT 'RawContig',
+  `parent` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_object_id`),
   KEY `id_idx` (`identifier`),
   KEY `anal_idx` (`analysis_id`),
@@ -854,20 +854,20 @@ CREATE TABLE `unmapped_object` (
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
-  `summary_description` varchar(255) DEFAULT NULL,
-  `full_description` varchar(255) DEFAULT NULL,
+  `summary_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
+  `full_description` varchar(255) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`unmapped_reason_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `external_db_id` int(11) NOT NULL,
-  `dbprimary_acc` varchar(512) NOT NULL,
-  `display_label` varchar(512) NOT NULL,
-  `version` varchar(10) DEFAULT NULL,
+  `dbprimary_acc` varchar(512) COLLATE latin1_bin NOT NULL,
+  `display_label` varchar(512) COLLATE latin1_bin NOT NULL,
+  `version` varchar(10) COLLATE latin1_bin DEFAULT NULL,
   `description` text COLLATE latin1_bin,
-  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') NOT NULL DEFAULT 'NONE',
-  `info_text` varchar(255) NOT NULL DEFAULT '',
+  `info_type` enum('NONE','PROJECTION','MISC','DEPENDENT','DIRECT','SEQUENCE_MATCH','INFERRED_PAIR','PROBE','UNMAPPED','CHECKSUM') COLLATE latin1_bin NOT NULL DEFAULT 'NONE',
+  `info_text` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`xref_id`),
   UNIQUE KEY `id_index` (`dbprimary_acc`,`external_db_id`,`info_type`,`info_text`,`version`),
   KEY `display_index` (`display_label`),
-- 
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