#!/usr/bin/perl
$filename = "sample";
open (TEXT, "sample.txt")||die"Cannot";
$line = " ";
$count = 0;
for $n (5..50)
   {
   $re = qr /[CAGT]{$n}/;
   $regexes[$n-5] = $re;
   }
NEXTLINE: while ($count < 1000)
   {
   $line = <TEXT> ;
   $count++;
   foreach my $value (@regexes)
      {
      $start = 0;
      while ($line =~ /$value/g)
         {
         $endline = $';
         $match = $&;
         $revmatch = reverse($match);
         $revmatch =~ tr/CAGT/GTCA/;
         if ($endline =~ /^([CAGT]{0,15})($revmatch)/)
            {
            $start = 1;
            $palindrome = $match . "*" . $1 . "*" . $2;
            $palhash{$palindrome}++;
            }
         }
      if ($start == 0)
         {
         goto NEXTLINE;
         }
      }
   }
open my $out, ">/DIR/results.txt"; 
close TEXT;
while(($key, $value) = each (%palhash))
   {
   print $out "$key => $value\n";
   }
exit;