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        $seq,    $ref,    $id,  $translate, $evalue,
        $format, $detail, $aug, $hmm,       $filter,
        $frag,   $subset, $organism
       ) = @_;
    my $mess = '* FASTA search for ' . $seq->display_id . "\n";
    my @hits = Bio::ORA->getHits($seq, 1, $ref);
    if ($#hits >= 0)
    {
        for (my $i = 0 ; $i <= $#hits ; $i++)
        {
            my ($hitstrand, $hitstart, $hitend) = split m/\|/, $hits[$i];
            my $seqstart = $hitstart - 250;
            $seqstart = 1 if ($seqstart < 1);
            my $seqend = $hitend + 250;
            $seqend = $seq->length() if ($seqend > $seq->length());
            my $seq_or = Bio::Seq->new(
                                  -seq      => $seq->subseq($seqstart, $seqend),
                                  -alphabet => 'dna',
                                  -id       => $seq->display_id . ":$seqstart-$seqend"
                                      );
            my $ora_obj = Bio::ORA->new($seq_or, $translate, $aug, $hmm);