diff --git a/misc-scripts/xref_mapping/gen_perc_file.pl b/misc-scripts/xref_mapping/gen_perc_file.pl
index 98baf92e3fdf3e2090b5af9aa6d31fe8ddf72027..a619d17c7d9c03b1b391a54b19ba79bdd970a6b3 100644
--- a/misc-scripts/xref_mapping/gen_perc_file.pl
+++ b/misc-scripts/xref_mapping/gen_perc_file.pl
@@ -47,14 +47,15 @@ foreach my $file (glob("$map_dir/*.map")) {
       = split(/:/, $_);
     
     if(defined($xref2acc{$query_id})){
-      $seen{$xref2acc{$query_id}} = 1;
       
       
       my $query_identity = int (100 * $identity / $query_length);
       my $target_identity = int (100 * $identity / $target_length);
       
-      print TEMP $query_identity."\t".$target_identity."\t".$xref2acc{$query_id}."\n";
-      
+      if(!defined($seen{$xref2acc{$query_id}})){
+	print TEMP $query_identity."\t".$target_identity."\t".$xref2acc{$query_id}."\n";
+      }
+      $seen{$xref2acc{$query_id}} = 1;
     }
     else{
       $count++;