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 62065f24431fc8bee897daa1b0ca5ac5813b4f91..8a242c15e45e87566cf6db973a659c0665e5bfbc 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 May  6 15:43:37 2016
+-- Created on Tue May 10 12:28:29 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/table.sql b/modules/t/test-genome-DBs/circ/core/table.sql
index 66cf6256780757e2f614045184363e4a37d52a9c..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/circ/core/table.sql
+++ b/modules/t/test-genome-DBs/circ/core/table.sql
@@ -34,8 +34,7 @@ CREATE TABLE `analysis` (
   `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`)
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
 ) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -103,7 +102,7 @@ CREATE TABLE `attrib_type` (
   `name` varchar(255) COLLATE latin1_bin NOT NULL DEFAULT '',
   `description` text COLLATE latin1_bin,
   PRIMARY KEY (`attrib_type_id`),
-  UNIQUE KEY `c` (`code`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM AUTO_INCREMENT=391 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `coord_system` (
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,7 +297,8 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -469,7 +474,7 @@ CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,7 +511,7 @@ CREATE TABLE `misc_set` (
   `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`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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`)
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
 ) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,8 +656,8 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=24117 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -690,8 +697,8 @@ CREATE TABLE `seq_region` (
   `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`)
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
 ) ENGINE=MyISAM AUTO_INCREMENT=14 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `seq_region_attrib` (
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,7 +724,8 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
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 767c1bbb503a745c095b5fc5b422fe4f57090ca2..86b57911436e1075bdb19df5870b75c024003075 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 May  6 15:43:56 2016
+-- Created on Tue May 10 12:28:58 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/table.sql b/modules/t/test-genome-DBs/homo_sapiens/core/table.sql
index 7a86d34792ed03382bb752199f5fb853a5bfe317..edab34555c34887837fa6702d3977f55e9d467ec 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 AUTO_INCREMENT=5 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `alt_allele_attrib` (
   `alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,7 +16,7 @@ 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 AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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 AUTO_INCREMENT=8409 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -73,7 +72,7 @@ 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 AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `associated_group` (
   `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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 AUTO_INCREMENT=20 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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 AUTO_INCREMENT=8 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,
@@ -144,7 +143,7 @@ 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 AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `density_type` (
   `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -154,7 +153,7 @@ CREATE TABLE `density_type` (
   `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 AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -172,7 +171,7 @@ CREATE TABLE `ditag` (
   `tag_count` smallint(6) DEFAULT '1',
   `sequence` text,
   PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3278357 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `ditag_feature` (
   `ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -190,8 +189,9 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4828763 DEFAULT CHARSET=latin1;
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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 AUTO_INCREMENT=29797140 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=162036 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=18277 DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -380,13 +384,13 @@ CREATE TABLE `karyotype` (
   `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -398,7 +402,7 @@ CREATE TABLE `mapping_session` (
   `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_set` (
   `mapping_set_id` int(10) unsigned NOT NULL,
@@ -418,8 +422,9 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
   `marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -432,7 +437,7 @@ 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 AUTO_INCREMENT=101 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -453,7 +458,7 @@ CREATE TABLE `marker_synonym` (
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1063 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -463,13 +468,13 @@ 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=137 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -489,7 +495,7 @@ 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 AUTO_INCREMENT=8 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_feature_misc_set` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -505,8 +511,8 @@ CREATE TABLE `misc_set` (
   `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 AUTO_INCREMENT=9 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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 AUTO_INCREMENT=253685 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -545,7 +552,7 @@ CREATE TABLE `operon` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `name_idx` (`display_label`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=2 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon_transcript` (
   `operon_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -564,7 +571,7 @@ CREATE TABLE `operon_transcript` (
   KEY `operon_idx` (`operon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon_transcript_gene` (
   `operon_transcript_id` int(10) unsigned DEFAULT NULL,
@@ -578,7 +585,7 @@ CREATE TABLE `peptide_archive` (
   `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=11 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_exon` (
   `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -594,7 +601,7 @@ 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 AUTO_INCREMENT=192 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_transcript` (
   `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -605,9 +612,9 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=18084 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `protein_align_feature` (
   `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -631,7 +638,7 @@ CREATE TABLE `protein_align_feature` (
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=11554505 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=242847 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,
@@ -665,7 +672,7 @@ CREATE TABLE `repeat_consensus` (
   KEY `class` (`repeat_class`),
   KEY `consensus` (`repeat_consensus`(10)),
   KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1018 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_feature` (
   `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,7 +689,7 @@ 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 AUTO_INCREMENT=922515 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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 AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,8 +724,9 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=4 DEFAULT CHARSET=latin1;
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=95700 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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21742 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=21742 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,17 +858,18 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=5 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `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 AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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 AUTO_INCREMENT=1000000 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/homo_sapiens/empty/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/SQLite/table.sql
index 11658fd075212d46a45852145fd9a0ec21bfe074..e6d6de444c9cabe4af5f7f32a8cba327fe247b12 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 May  6 15:44:14 2016
+-- Created on Tue May 10 12:29:23 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/empty/table.sql b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
index 00154a21337ebcf9ebad8cd5b52082daad297b74..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
+++ b/modules/t/test-genome-DBs/homo_sapiens/empty/table.sql
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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 AUTO_INCREMENT=1504 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -73,7 +72,7 @@ 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 AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `associated_group` (
   `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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 AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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 AUTO_INCREMENT=8 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,
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   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',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -463,13 +468,13 @@ 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=126 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,7 +511,7 @@ CREATE TABLE `misc_set` (
   `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`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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 AUTO_INCREMENT=965907 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,8 +724,9 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3 DEFAULT CHARSET=latin1;
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ 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',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   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',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -857,7 +869,7 @@ CREATE TABLE `unmapped_reason` (
   `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 AUTO_INCREMENT=3 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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/homo_sapiens/patch/SQLite/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/SQLite/table.sql
index 0f982fa109eb9f77d6d3b0deb34f84e3d0a2a019..1a7e71d665000b4e2d35f286faf3c4e83ecc0d5f 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 May  6 15:44:32 2016
+-- Created on Tue May 10 12:29:49 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/patch/table.sql b/modules/t/test-genome-DBs/homo_sapiens/patch/table.sql
index abe35683041e94bbb7c7ee432c3e3c9abcebd98b..edab34555c34887837fa6702d3977f55e9d467ec 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 AUTO_INCREMENT=11 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `alt_allele_attrib` (
   `alt_allele_id` int(10) unsigned DEFAULT NULL,
@@ -16,7 +16,7 @@ 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 AUTO_INCREMENT=5213 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `analysis` (
   `analysis_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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 AUTO_INCREMENT=8449 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -73,7 +72,7 @@ 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 AUTO_INCREMENT=155 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `associated_group` (
   `associated_group_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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 AUTO_INCREMENT=405 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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 AUTO_INCREMENT=1004 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,
@@ -144,7 +143,7 @@ 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 AUTO_INCREMENT=16758826 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `density_type` (
   `density_type_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -154,7 +153,7 @@ CREATE TABLE `density_type` (
   `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 AUTO_INCREMENT=110 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -172,7 +171,7 @@ CREATE TABLE `ditag` (
   `tag_count` smallint(6) DEFAULT '1',
   `sequence` text,
   PRIMARY KEY (`ditag_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1366612 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `ditag_feature` (
   `ditag_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -190,8 +189,9 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=1221449 DEFAULT CHARSET=latin1;
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
   `seq_region_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -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 AUTO_INCREMENT=29387404 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=7296966 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=633706 DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -332,7 +336,7 @@ 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 AUTO_INCREMENT=71 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `identity_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -380,13 +384,13 @@ CREATE TABLE `karyotype` (
   `stain` varchar(40) COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`karyotype_id`),
   KEY `region_band_idx` (`seq_region_id`,`band`)
-) ENGINE=MyISAM AUTO_INCREMENT=852 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `map` (
   `map_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `map_name` varchar(30) COLLATE latin1_bin NOT NULL DEFAULT '',
   PRIMARY KEY (`map_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=13 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_session` (
   `mapping_session_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -398,7 +402,7 @@ CREATE TABLE `mapping_session` (
   `new_assembly` varchar(20) COLLATE latin1_bin NOT NULL DEFAULT '',
   `created` datetime NOT NULL,
   PRIMARY KEY (`mapping_session_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=394 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `mapping_set` (
   `mapping_set_id` int(10) unsigned NOT NULL,
@@ -418,8 +422,9 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
-) ENGINE=MyISAM AUTO_INCREMENT=27 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
   `marker_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -432,7 +437,7 @@ 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 AUTO_INCREMENT=27 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_map_location` (
   `marker_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -453,7 +458,7 @@ CREATE TABLE `marker_synonym` (
   PRIMARY KEY (`marker_synonym_id`),
   KEY `marker_synonym_idx` (`marker_synonym_id`,`name`),
   KEY `marker_idx` (`marker_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=716771 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `meta` (
   `meta_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -463,13 +468,13 @@ 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=2089 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -489,7 +495,7 @@ 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 AUTO_INCREMENT=93001 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_feature_misc_set` (
   `misc_feature_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -505,8 +511,8 @@ CREATE TABLE `misc_set` (
   `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 AUTO_INCREMENT=19 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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 AUTO_INCREMENT=17375428 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -578,7 +585,7 @@ CREATE TABLE `peptide_archive` (
   `peptide_seq` mediumtext COLLATE latin1_bin NOT NULL,
   PRIMARY KEY (`peptide_archive_id`),
   KEY `checksum` (`md5_checksum`)
-) ENGINE=MyISAM AUTO_INCREMENT=250655 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_exon` (
   `prediction_exon_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -594,7 +601,7 @@ 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 AUTO_INCREMENT=394607 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `prediction_transcript` (
   `prediction_transcript_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -605,9 +612,9 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=54799 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `protein_align_feature` (
   `protein_align_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -631,7 +638,7 @@ CREATE TABLE `protein_align_feature` (
   KEY `hit_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `external_db_idx` (`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=19573639 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=7821872 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,
@@ -665,7 +672,7 @@ CREATE TABLE `repeat_consensus` (
   KEY `class` (`repeat_class`),
   KEY `consensus` (`repeat_consensus`(10)),
   KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=595635 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_feature` (
   `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,7 +689,7 @@ 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 AUTO_INCREMENT=31576665 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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 AUTO_INCREMENT=1001161224 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,8 +724,9 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=177 DEFAULT CHARSET=latin1;
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
   `simple_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `hit_idx` (`display_label`)
-) ENGINE=MyISAM AUTO_INCREMENT=968471 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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=2047756 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=1044748 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,17 +858,18 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=12401901 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `unmapped_reason` (
   `unmapped_reason_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
   `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 AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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 AUTO_INCREMENT=7795492 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/mapping/core/SQLite/table.sql b/modules/t/test-genome-DBs/mapping/core/SQLite/table.sql
index f36902d0a12f8531c03035a94adfb93157162877..da80bb4458582ae13aa6fdabf5753179c77968ab 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 May  6 15:45:03 2016
+-- Created on Tue May 10 12:30:30 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/table.sql b/modules/t/test-genome-DBs/mapping/core/table.sql
index 6ec8041323014f6cc819624d25684faf53e55b62..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/mapping/core/table.sql
+++ b/modules/t/test-genome-DBs/mapping/core/table.sql
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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 AUTO_INCREMENT=2 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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 AUTO_INCREMENT=3 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,
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   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',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -463,13 +468,13 @@ 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=131 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,7 +511,7 @@ CREATE TABLE `misc_set` (
   `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`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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 AUTO_INCREMENT=5 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,7 +724,8 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ 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',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   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',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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/mus_musculus/core/SQLite/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/SQLite/table.sql
index b64a483a8b1d4c855f81d2a60ae083a51039d894..d19c7d2e33ba7928615813e6458205c157a6e2de 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 May  6 15:45:20 2016
+-- Created on Tue May 10 12:30:52 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/mus_musculus/core/table.sql b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
index 27f6bfac4c923c648936a9704372093e3593e604..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/mus_musculus/core/table.sql
+++ b/modules/t/test-genome-DBs/mus_musculus/core/table.sql
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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 AUTO_INCREMENT=508 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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 AUTO_INCREMENT=112 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,
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   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',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -463,13 +468,13 @@ 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=1667 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,7 +511,7 @@ CREATE TABLE `misc_set` (
   `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`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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 AUTO_INCREMENT=20603 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,7 +724,8 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ 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',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   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',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -857,7 +869,7 @@ CREATE TABLE `unmapped_reason` (
   `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 AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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/nameless/core/SQLite/table.sql b/modules/t/test-genome-DBs/nameless/core/SQLite/table.sql
index da72638f235bb4280cb3e42e51dc5cbf8cec8819..6969352d60d92350f1100d186d15164e32cf7ce8 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 May  6 15:45:48 2016
+-- Created on Tue May 10 12:31:29 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/table.sql b/modules/t/test-genome-DBs/nameless/core/table.sql
index 462b6322690320a0007a245a5f0021f9eb70a6ce..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/nameless/core/table.sql
+++ b/modules/t/test-genome-DBs/nameless/core/table.sql
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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,
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   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',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -463,13 +468,13 @@ 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=130 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,7 +511,7 @@ CREATE TABLE `misc_set` (
   `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`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,7 +724,8 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ 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',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   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',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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/polyploidy/core/SQLite/table.sql b/modules/t/test-genome-DBs/polyploidy/core/SQLite/table.sql
index d6564ea744e831c38f849ba0ed892d8b51d4280f..1954b748f7a1f6051a9cc5421d25fd3d968cf1d5 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 May  6 15:46:11 2016
+-- Created on Tue May 10 12:31:56 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/table.sql b/modules/t/test-genome-DBs/polyploidy/core/table.sql
index 0b0a206c970257f243153943e164e65e3b582a84..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/polyploidy/core/table.sql
+++ b/modules/t/test-genome-DBs/polyploidy/core/table.sql
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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 AUTO_INCREMENT=201 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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 AUTO_INCREMENT=437 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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 AUTO_INCREMENT=11 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,
@@ -154,7 +153,7 @@ CREATE TABLE `density_type` (
   `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 AUTO_INCREMENT=23 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `dependent_xref` (
   `object_xref_id` int(10) unsigned NOT NULL,
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   PRIMARY KEY (`exon_id`),
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=382467 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `exon_transcript` (
   `exon_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=40234 DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -332,7 +336,7 @@ 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 AUTO_INCREMENT=45 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `identity_xref` (
   `object_xref_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -463,13 +468,13 @@ 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=211 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,8 +511,8 @@ CREATE TABLE `misc_set` (
   `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 AUTO_INCREMENT=24 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `code_idx` (`code`)
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
   `object_xref_id` int(11) NOT NULL AUTO_INCREMENT,
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`hit_name`),
   KEY `analysis_idx` (`analysis_id`)
-) ENGINE=MyISAM AUTO_INCREMENT=3502933 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,
@@ -665,7 +672,7 @@ CREATE TABLE `repeat_consensus` (
   KEY `class` (`repeat_class`),
   KEY `consensus` (`repeat_consensus`(10)),
   KEY `type` (`repeat_type`)
-) ENGINE=MyISAM AUTO_INCREMENT=1163919 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `repeat_feature` (
   `repeat_feature_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -682,7 +689,7 @@ 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 AUTO_INCREMENT=10446798 DEFAULT CHARSET=latin1 COLLATE=latin1_bin MAX_ROWS=100000000 AVG_ROW_LENGTH=80;
+) ENGINE=MyISAM 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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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 AUTO_INCREMENT=3495795 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,7 +724,8 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ CREATE TABLE `transcript` (
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `transcript_attrib` (
   `transcript_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   PRIMARY KEY (`translation_id`),
   KEY `transcript_idx` (`transcript_id`),
   KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM AUTO_INCREMENT=124988 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=6690 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `translation_attrib` (
   `translation_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -857,7 +869,7 @@ CREATE TABLE `unmapped_reason` (
   `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 AUTO_INCREMENT=139 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
+) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `xref` (
   `xref_id` int(10) unsigned NOT NULL AUTO_INCREMENT,
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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/test_collection/core/SQLite/table.sql b/modules/t/test-genome-DBs/test_collection/core/SQLite/table.sql
index 2430ff36ca2b76acbfcfb75e22385ce80ece3aaf..60e2148a428e527995f24e7b252a827f4c35a191 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 May  6 15:46:27 2016
+-- Created on Tue May 10 12:32:17 2016
 -- 
 
 BEGIN TRANSACTION;
@@ -51,7 +51,7 @@ CREATE TABLE analysis (
   gff_feature varchar(40)
 );
 
-CREATE UNIQUE INDEX logic_name ON analysis (logic_name);
+CREATE UNIQUE INDEX logic_name_idx ON analysis (logic_name);
 
 --
 -- Table: analysis_description
@@ -64,6 +64,8 @@ CREATE TABLE analysis_description (
   web_data text
 );
 
+CREATE UNIQUE INDEX analysis_idx ON analysis_description (analysis_id);
+
 --
 -- Table: assembly
 --
@@ -127,7 +129,7 @@ CREATE TABLE attrib_type (
   description text
 );
 
-CREATE UNIQUE INDEX c ON attrib_type (code);
+CREATE UNIQUE INDEX code_idx ON attrib_type (code);
 
 --
 -- Table: coord_system
@@ -301,6 +303,8 @@ CREATE TABLE external_db (
   description text
 );
 
+CREATE UNIQUE INDEX db_name_db_release_idx ON external_db (db_name, db_release);
+
 --
 -- Table: external_synonym
 --
@@ -396,7 +400,7 @@ CREATE TABLE interpro (
   id varchar(40) NOT NULL DEFAULT ''
 );
 
-CREATE UNIQUE INDEX interpro_ac ON interpro (interpro_ac, id);
+CREATE UNIQUE INDEX accession_idx ON interpro (interpro_ac, id);
 
 --
 -- Table: intron_supporting_evidence
@@ -532,7 +536,7 @@ CREATE TABLE meta_coord (
   max_length integer
 );
 
-CREATE UNIQUE INDEX table_name ON meta_coord (table_name, coord_system_id);
+CREATE UNIQUE INDEX cs_table_name_idx ON meta_coord (coord_system_id, table_name);
 
 --
 -- Table: misc_attrib
@@ -576,13 +580,13 @@ CREATE TABLE misc_set (
   max_length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX c02 ON misc_set (code);
+CREATE UNIQUE INDEX code_idx02 ON misc_set (code);
 
 --
 -- Table: object_xref
 --
 CREATE TABLE object_xref (
-  object_xref_id integer NOT NULL,
+  object_xref_id INTEGER PRIMARY KEY AUTOINCREMENT NOT NULL,
   ensembl_id integer NOT NULL DEFAULT 0,
   ensembl_object_type enum NOT NULL DEFAULT 'RawContig',
   xref_id integer NOT NULL,
@@ -590,7 +594,7 @@ CREATE TABLE object_xref (
   analysis_id smallint NOT NULL
 );
 
-CREATE UNIQUE INDEX ensembl_object_type ON object_xref (ensembl_object_type, ensembl_id, xref_id);
+CREATE UNIQUE INDEX xref_idx ON object_xref (xref_id, ensembl_object_type, ensembl_id, analysis_id);
 
 --
 -- Table: ontology_xref
@@ -601,7 +605,7 @@ CREATE TABLE ontology_xref (
   source_xref_id integer
 );
 
-CREATE UNIQUE INDEX object_xref_id_2 ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
+CREATE UNIQUE INDEX object_source_type_idx ON ontology_xref (object_xref_id, source_xref_id, linkage_type);
 
 --
 -- Table: operon
@@ -763,7 +767,7 @@ CREATE TABLE seq_region (
   length integer NOT NULL DEFAULT 0
 );
 
-CREATE UNIQUE INDEX coord_system_id ON seq_region (coord_system_id, name);
+CREATE UNIQUE INDEX name_cs_idx ON seq_region (name, coord_system_id);
 
 --
 -- Table: seq_region_attrib
@@ -940,6 +944,8 @@ 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/table.sql b/modules/t/test-genome-DBs/test_collection/core/table.sql
index 9150552e0a72e130833221b40ed3376e533e8554..edab34555c34887837fa6702d3977f55e9d467ec 100644
--- a/modules/t/test-genome-DBs/test_collection/core/table.sql
+++ b/modules/t/test-genome-DBs/test_collection/core/table.sql
@@ -34,9 +34,8 @@ CREATE TABLE `analysis` (
   `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;
+  UNIQUE KEY `logic_name_idx` (`logic_name`)
+) ENGINE=MyISAM AUTO_INCREMENT=39 DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `analysis_description` (
   `analysis_id` int(10) unsigned NOT NULL DEFAULT '0',
@@ -44,7 +43,7 @@ CREATE TABLE `analysis_description` (
   `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`)
+  UNIQUE KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `assembly` (
@@ -103,8 +102,8 @@ CREATE TABLE `attrib_type` (
   `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;
+  UNIQUE KEY `code_idx` (`code`)
+) 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 +116,7 @@ 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,
@@ -190,7 +189,8 @@ CREATE TABLE `ditag_feature` (
   `ditag_side` char(1) DEFAULT '',
   PRIMARY KEY (`ditag_feature_id`),
   KEY `ditag_id` (`ditag_id`),
-  KEY `ditag_pair_id` (`ditag_pair_id`)
+  KEY `ditag_pair_id` (`ditag_pair_id`),
+  KEY `seq_region_idx` (`seq_region_id`, `seq_region_start`, `seq_region_end`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `dna` (
@@ -242,7 +242,7 @@ CREATE TABLE `exon` (
   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',
@@ -264,7 +264,8 @@ CREATE TABLE `external_db` (
   `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`)
+  PRIMARY KEY (`external_db_id`),
+  UNIQUE KEY `db_name_db_release_idx` (`db_name`,`db_release`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `external_synonym` (
@@ -284,7 +285,7 @@ CREATE TABLE `gene` (
   `seq_region_strand` tinyint(2) NOT NULL,
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_transcript_id` int(10) unsigned NOT NULL,
@@ -296,8 +297,9 @@ CREATE TABLE `gene` (
   KEY `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `xref_id_index` (`display_xref_id`),
   KEY `analysis_idx` (`analysis_id`),
-  KEY `stable_id_idx` (`stable_id`,`version`)
-) ENGINE=MyISAM DEFAULT CHARSET=latin1;
+  KEY `stable_id_idx` (`stable_id`,`version`),
+  KEY `canonical_transcript_id_idx` (`canonical_transcript_id`)
+) ENGINE=MyISAM AUTO_INCREMENT=6885 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `gene_archive` (
   `gene_stable_id` varchar(128) COLLATE latin1_bin NOT NULL DEFAULT '',
@@ -310,7 +312,8 @@ CREATE TABLE `gene_archive` (
   `mapping_session_id` int(11) NOT NULL DEFAULT '0',
   KEY `gene_idx` (`gene_stable_id`,`gene_version`),
   KEY `transcript_idx` (`transcript_stable_id`,`transcript_version`),
-  KEY `translation_idx` (`translation_stable_id`,`translation_version`)
+  KEY `translation_idx` (`translation_stable_id`,`translation_version`),
+  KEY `peptide_archive_id_idx` (`peptide_archive_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `gene_attrib` (
@@ -319,6 +322,7 @@ CREATE TABLE `gene_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `gene_idx` (`gene_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -351,8 +355,8 @@ CREATE TABLE `identity_xref` (
 CREATE TABLE `interpro` (
   `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`)
+  UNIQUE KEY `accession_idx` (`interpro_ac`,`id`),
+  KEY `id_idx` (`id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `intron_supporting_evidence` (
@@ -418,7 +422,8 @@ CREATE TABLE `marker` (
   `priority` int(11) DEFAULT NULL,
   `type` enum('est','microsatellite') COLLATE latin1_bin DEFAULT NULL,
   PRIMARY KEY (`marker_id`),
-  KEY `marker_idx` (`marker_id`,`priority`)
+  KEY `marker_idx` (`marker_id`,`priority`),
+  KEY `display_idx` (`display_marker_synonym_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `marker_feature` (
@@ -463,13 +468,13 @@ 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=193 DEFAULT CHARSET=latin1;
+) ENGINE=MyISAM AUTO_INCREMENT=98 DEFAULT CHARSET=latin1;
 
 CREATE TABLE `meta_coord` (
   `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`)
+  UNIQUE KEY `cs_table_name_idx` (`coord_system_id`,`table_name`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `misc_attrib` (
@@ -478,6 +483,7 @@ CREATE TABLE `misc_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `misc_feature_idx` (`misc_feature_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -505,7 +511,7 @@ CREATE TABLE `misc_set` (
   `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`)
+  UNIQUE KEY `code_idx` (`code`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
 CREATE TABLE `object_xref` (
@@ -515,18 +521,19 @@ CREATE TABLE `object_xref` (
   `xref_id` int(10) unsigned NOT 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;
+  PRIMARY KEY (`object_xref_id`),
+  UNIQUE KEY `xref_idx` (`xref_id`, `ensembl_object_type`, `ensembl_id`, `analysis_id`),
+  KEY `ensembl_idx` (`ensembl_object_type`, `ensembl_id`),
+  KEY `analysis_idx` (`analysis_id`)
+) 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',
   `linkage_type` varchar(3) DEFAULT NULL,
   `source_xref_id` int(10) unsigned DEFAULT NULL,
-  UNIQUE KEY `object_xref_id_2` (`object_xref_id`,`source_xref_id`,`linkage_type`),
-  KEY `object_xref_id` (`object_xref_id`),
-  KEY `source_xref_id` (`source_xref_id`)
+  UNIQUE KEY `object_source_type_idx` (`object_xref_id`,`source_xref_id`,`linkage_type`),
+  KEY `object_idx` (`object_xref_id`),
+  KEY `source_idx` (`source_xref_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `operon` (
@@ -605,7 +612,7 @@ CREATE TABLE `prediction_transcript` (
   `analysis_id` int(11) 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 `seq_region_idx` (`seq_region_id`,`seq_region_start`),
   KEY `analysis_idx` (`analysis_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -649,10 +656,10 @@ CREATE TABLE `protein_feature` (
   `hit_description` text COLLATE latin1_bin,
   PRIMARY KEY (`protein_feature_id`),
   UNIQUE KEY `aln_idx` (`translation_id`,`hit_name`,`seq_start`,`seq_end`,`hit_start`,`hit_end`),
-  KEY `translation_id` (`translation_id`),
-  KEY `hitname_index` (`hit_name`),
+  KEY `translation_idx` (`translation_id`),
+  KEY `hitname_idx` (`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,
@@ -690,9 +697,9 @@ CREATE TABLE `seq_region` (
   `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;
+  UNIQUE KEY `name_cs_idx` (`name`,`coord_system_id`),
+  KEY `cs_idx` (`coord_system_id`)
+) 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',
@@ -700,6 +707,7 @@ CREATE TABLE `seq_region_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -707,7 +715,7 @@ CREATE TABLE `seq_region_mapping` (
   `external_seq_region_id` int(10) unsigned NOT NULL,
   `internal_seq_region_id` int(10) unsigned NOT NULL,
   `mapping_set_id` int(10) unsigned NOT NULL,
-  KEY `mapping_set_id` (`mapping_set_id`)
+  KEY `mapping_set_idx` (`mapping_set_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `seq_region_synonym` (
@@ -716,7 +724,8 @@ CREATE TABLE `seq_region_synonym` (
   `synonym` varchar(250) NOT NULL,
   `external_db_id` smallint(5) unsigned DEFAULT NULL,
   PRIMARY KEY (`seq_region_synonym_id`),
-  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`)
+  UNIQUE KEY `syn_idx` (`synonym`,`seq_region_id`),
+  KEY `seq_region_idx` (`seq_region_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1;
 
 CREATE TABLE `simple_feature` (
@@ -732,7 +741,7 @@ CREATE TABLE `simple_feature` (
   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) COLLATE latin1_bin DEFAULT NULL,
@@ -766,7 +775,7 @@ CREATE TABLE `transcript` (
   `display_xref_id` int(10) unsigned DEFAULT NULL,
   `source` varchar(40) NOT NULL DEFAULT 'ensembl',
   `biotype` varchar(40) NOT NULL,
-  `status` enum('KNOWN','NOVEL','PUTATIVE','PREDICTED','KNOWN_BY_PROJECTION','UNKNOWN') DEFAULT NULL,
+  `status` enum('KNOWN', 'NOVEL', 'PUTATIVE', 'PREDICTED', 'KNOWN_BY_PROJECTION', 'UNKNOWN', 'ANNOTATED') DEFAULT NULL,
   `description` text,
   `is_current` tinyint(1) NOT NULL DEFAULT '1',
   `canonical_translation_id` int(10) unsigned DEFAULT NULL,
@@ -781,7 +790,7 @@ 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',
@@ -789,6 +798,7 @@ CREATE TABLE `transcript_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `transcript_idx` (`transcript_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -823,7 +833,7 @@ CREATE TABLE `translation` (
   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',
@@ -831,6 +841,7 @@ CREATE TABLE `translation_attrib` (
   `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 `val_only_idx` (`value`(40)),
   KEY `translation_idx` (`translation_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -847,8 +858,9 @@ CREATE TABLE `unmapped_object` (
   `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`),
+  UNIQUE KEY `unique_unmapped_obj_idx` (`ensembl_id`, `ensembl_object_type`, `identifier`, `unmapped_reason_id`, `parent`, `external_db_id`),
+  KEY `id_idx` (`identifier`(50)),
+  KEY `ext_db_identifier_idx` (`external_db_id`, `identifier`),
   KEY `anal_exdb_idx` (`analysis_id`,`external_db_id`)
 ) ENGINE=MyISAM DEFAULT CHARSET=latin1 COLLATE=latin1_bin;
 
@@ -872,5 +884,5 @@ CREATE TABLE `xref` (
   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;