diff --git a/scripts/promer.pl b/scripts/promer.pl
index 8932515..756ecb4 100644
--- a/scripts/promer.pl
+++ b/scripts/promer.pl
@@ -346,6 +346,8 @@ ( )
 
     #-- Run postpro and assert return value is zero
     print (STDERR "4: FINISHING DATA\n");
+    sort_mgaps("$qry_file","$pfx.mgaps");
+
     $err[0] = $tigr->runCommand
 	("$postpro_path $psw -x $blsm -b $blen ".
 	 "$ref_file $qry_file $pfx < $pfx.mgaps");
@@ -379,4 +381,68 @@ ( )
 
 exit ( main ( ) );
 
+sub sort_mgaps {
+    # Input, file names, strings
+    my $qry = shift;
+    my $mgaps = shift;
+    # read query file
+    my @qry_entries = ();
+    my $fh;
+    open($fh, "$qry") || die "couldn't read file $qry\n";
+    while(my $line = <$fh>) {
+	chomp $line;
+	next unless $line=~/^\>(\S+)/;
+	push(@qry_entries,$1);
+    }
+    close($fh);
+    # read mgaps file
+    my %mgaps_lines = ();
+    my %dna_pep = (); # used to look up the peptides in a dna seq
+    open($fh, "$mgaps") || die "couldn't read file $mgaps\n";
+    my $pos = 0;
+    my $pos_old = $pos;
+    my $cur_entry = ""; # e.g. 3210101.5
+    while(1) {
+	my $line=<$fh>;
+	last unless defined $line;
+	chomp $line;
+	if($line=~/^\>\s*(\S+)/) {
+	    $cur_entry = $1;
+	    # find out the corresponding dna id in query file
+	    die "wrong format $cur_entry\n"
+		unless $cur_entry=~/^(.+)\.[\d+]$/;
+	    my $dna = $1;
+	    if(exists($dna_pep{$dna})) {
+		push(@{$dna_pep{$dna}},$cur_entry);
+	    }
+	    else {
+		$dna_pep{$dna} = [$cur_entry];
+	    }
+	    # find out the lines corresponding to the current entry
+	    if(exists($mgaps_lines{$cur_entry})) {
+		push(@{$mgaps_lines{$cur_entry}},"$line\n");
+	    }
+	    else {
+		$mgaps_lines{$cur_entry} = ["$line\n"];
+	    }
+	}
+	else {
+	    push(@{$mgaps_lines{$cur_entry}},"$line\n");
+	}
+    }
+    close($fh);
+    # sort the query file
+    open($fh,">$mgaps") || die "couldn't write to file $mgaps\n";
+    my $oldfh = select($fh);
+    foreach my $dna (@qry_entries) {
+	foreach my $pep (@{$dna_pep{$dna}}) {
+	    my $ref_line = $mgaps_lines{$pep};
+	    foreach my $line(@{$ref_line}) {
+		print $line;
+	    }
+	}
+    }
+    select($oldfh);
+    close($fh);
+}
 #-- END OF SCRIPT