diff --git a/misc-scripts/probe_mapping/compare_mappings.pl b/misc-scripts/probe_mapping/compare_mappings.pl
index 14d222a8baaad4135e92472f9b6e80b9372e6ff7..3acf66e043bf49120d8e79765142488161a31b21 100644
--- a/misc-scripts/probe_mapping/compare_mappings.pl
+++ b/misc-scripts/probe_mapping/compare_mappings.pl
@@ -6,7 +6,7 @@ use Bio::EnsEMBL::DBEntry;
 use Bio::EnsEMBL::DBSQL::DBAdaptor;
 use Bio::EnsEMBL::Mapper::RangeRegistry;
 
-my ($s_host, $s_port, $s_user, $s_pass, $s_dbname, $t_host, $t_port, $t_user, $t_pass, $t_dbname, );
+my ($s_host, $s_port, $s_user, $s_pass, $s_dbname, $t_host, $t_port, $t_user, $t_pass, $t_dbname, $array);
 
 GetOptions('source_host=s'      => \$s_host,
            'source_user=s'      => \$s_user,
@@ -18,11 +18,16 @@ GetOptions('source_host=s'      => \$s_host,
            'target_port=i'      => \$t_port,
            'target_pass=s'      => \$t_pass,
            'target_dbname=s'    => \$t_dbname,
+	   'array=s'            => \$array,
            'help'               => sub { usage(); exit(0); });
 
 $s_port ||= 3306; $t_port ||= 3306;
 
-usage() if(!$s_user || !$s_dbname || !$s_host || !$t_user || !$t_dbname || !$t_host);
+usage() if(!$s_user || !$s_dbname || !$s_host || !$t_dbname);
+
+$t_host = $s_host if (!$t_host);
+$t_port = $s_port if (!$t_port);
+$t_user = $s_user if (!$t_user);
 
 my $s_db = new Bio::EnsEMBL::DBSQL::DBAdaptor('-host'   => $s_host,
 					      '-port'   => $s_port,
@@ -40,13 +45,17 @@ my $t_db = new Bio::EnsEMBL::DBSQL::DBAdaptor('-host'   => $t_host,
 
 # TODO fix this when external db is sorted out
 my $restrict_sql = "x.external_db_id > 3000 AND x.external_db_id < 3210";
+$restrict_sql = " e.db_name='$array'" if ($array);
 
 run();
 
 sub run {
 
+  print "Using only array $array\n" if ($array);
+
   # compare total counts first
-  my $count_sql = "SELECT COUNT(*) FROM xref x, object_xref ox WHERE x.xref_id=ox.xref_id AND ox.ensembl_object_type='Transcript' AND $restrict_sql";
+  my $count_sql = "SELECT COUNT(*) FROM xref x, object_xref ox, external_db e WHERE e.external_db_id=x.external_db_id AND x.xref_id=ox.xref_id AND ox.ensembl_object_type='Transcript' AND $restrict_sql";
+
   my $s_sth = $s_db->dbc()->prepare($count_sql);
   $s_sth->execute();
   my $count = ($s_sth->fetchrow_array())[0];
@@ -55,7 +64,7 @@ sub run {
   my $t_sth = $t_db->dbc()->prepare($count_sql);
   $t_sth->execute();
   $count = ($t_sth->fetchrow_array())[0];
-  print "Total oligo_xrefs in $t_dbname: $count\n";
+  print "Total oligo xrefs in $t_dbname: $count\n";
 
   # cache all mappings from each database
   # key format: transcript_stable_id:array:probe
@@ -103,7 +112,7 @@ sub run {
 
 sub cache_mappings {
 
-  my ($db) = @_;
+  my ($db, $print) = @_;
 
   my %mappings;
 
@@ -112,10 +121,12 @@ sub cache_mappings {
   $sth->execute();
   while (my @row = $sth->fetchrow_array()) {
 
-    #my $key = $row[0] . ":" . $row[1]. ":" . $row[2]; # TODO - add array back in
-    my $key = $row[0] . ":" . $row[2];
+    my $key = $row[0] . "\t" . $row[1]. "\t" . $row[2];
+    #my $key = $row[0] . "\t" . $row[2];
     $mappings{$key} = $key;
 
+    print "$key\n" if ($print);
+
   }
 
   $sth->finish();
@@ -151,10 +162,11 @@ sub usage {
   NEW XREFS:
 
    --target_host          The database server to read the second set of xrefs from.
+                          Defaults to source_host.
 		
-   [--target_port]        The port to use.. Defaults to 3306.
+   [--target_port]        The port to use. Defaults to 3306.
 		
-   --target_user          Database username.
+   --target_user          Database username. Defaults to source_user.
 		
    --target_pass          Password for target_user, if required.
 		
@@ -162,6 +174,8 @@ sub usage {
 
   MISCELLANEOUS:
 
+  [--array]           Just compare results from this array.
+
   [--help]            This text.