foreach my $l (@file)  {

    if (($l =~ /^>(\w{2})(.{1})(\w{2}\d{6}.{2})(\D?)(\d+)(\W{1})(\d+)/))   {

        $current =  undef;

        if ($4)   {
            $hit = "$7-$5";
        }

        else {
             $hit = "$5-$7";
        }
}

    foreach my $k (@positions)   {
        if ($k == $hit)  {
            $in_gene = 1;
        }
    }

     if ($in_gene)   {
          $gene .= $l;
     }

     unless ($l =~ /^>/)  {
         next;
     }

}
print $gene;