#!/usr/bin/perl

open (TEXT, "sample.txt")||die"Cannot";
my $pat=qr'^(Contig +([0-9]*))\s';
my $count = 0;
for my $n (5..20)
   {
   my $re = qr /[CAGU]{$n}/;
   $regexes[$n-5] = $re;
   }
NEXTLINE: while ($count < 1000)
   {
   my $line = <TEXT> ;
   $count++;
   foreach my $value (@regexes)
      {
      my $start = 0;

      while ($line =~ /$value/g)
         {
        my $endline = $';
        my $match = $&;
        my $revmatch = reverse($match);
         $revmatch =~ tr/CAGU/GUCA/;
         if ($endline =~ /^([CAGU]{0,15})($revmatch)/)
            {
            $start = 1;
          my $palindrome = $match . "*" . $1 . "*" . $2;
            $palhash{$palindrome}++;
            }
         }
      if ($start == 0)
         {
         goto NEXTLINE;
         }
	 }
   }
print "L.$pat\n";
close TEXT;
while(($key, $value) = each (%palhash))
   {
print "$key => $value\n";
   }
exit;

##</code><code>##

Contig1
NAAAAGUAUAGGCUCGAGAGAGAAGUCCUGGCCUAUCGGAUUACACCACGNGUCAGAUCU
GUCACUUCAAGGAGCUUUUCAGCGUCUUUGACAAGAAUGGCNGACGGUUGCCGUCCUUCC
AGGGAGAUUGGGGCAGAAUUCGAGUCACUGCCNGUGGAUUCCUUAGUGAUCCAGAUGUCG
GAUAUAUGUCCAAUAUAGCCAAUNGUUGUUGGACAUAGCACCAUCAAUCAUCAAGAUUGC
UAUUUCGCCACCUCNAUGUAGAGUGGAAGAUCCAAAUGCGGGAAUGGAUUUCAAGGUUGG
UUAAGNAUGGGGGCAGCGGAUGAGUUAACAGUACAGCAAGCUAGGCAGCUCCAUUUNUGA
CUUGGAAUCUUCAUACGAUUCAUUUAUGGCAGCUUUGCCUAAUGUUGNGUACUUGAAAGU
AAAAUCCAAUAUUUCCAUAUUUUUGUUUAGUGCUUCAAAUCUGGUGAGAACGGAUGUUUU
AAGUUGGUAAAACAGUGUAUUCAUUUUGAAGAGUUCUUGGAUUGUUUAAAGCUCAAGAUG
CUAUUUGUGUGCUGCUGAUUUGUCGUUCUAUGAGAAAGAAUAUAUGCUUUAAUUUGGUUU
UGUAAUAUUAANUAUAUUCAUUCCCCUUGAUUGUUGUUUUGUNNNNNNNNNNNNNNNNNN
NN
Contig2
NUGUUUUUUCUUUACUCGGUGUCUCGUCGGUACUCGACGACUAAANGGGNUAUAGGAGGG
GCGCGAACGNCGAAACGGGAGUGGGUACAAAGCGUGGUCCNGGAUAGACGAGAGCGGACG
CGCCGGGUGAAGCUCGGCGCGACGCGAGGCANAGAGGGGCCCGCAGANNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNAAGNCCCAGGAUGCGCAUCGCCCCAGGGGUGAAACCCCCAUCCCAAAGAA
UGCUNCUCCUNCGCGGUAGGGCAGCUNCCCGAAGCACCCGACCGCUUUNAGGCCANCCAU
AUGAUAAAGNAACGUUGUGUGGUGAAUGGGAUGAAGAUGAUUGAAGNAGAGUAGAGUUUU
GCCUCUANAUCUUGAUAUGUAUAUCUUUAAUUAUAUAANUAUAGCUCAUUAUAUUGUGCN
UUAGCAUGUAAUAUUUAAGUCUAAAAUUAANUGGACCUCAGCUCGAGGUCGNCAUUCUUU
GUUACUUUAGAUCAGAUCUGUANUUCCCUUUGUAUUGUUCAGGNUUUCCAACCAUAAAUU
AUUGGUACUAUCUUNAUUGUUAUCAUAAUUGACGUGUGUUUAAGUUCNNNNNNNNNNNNN
NNNNN

##</code><code>##

Contig1
GACGG*UUG*CCGUC => 1
GAUGC**GCAUC => 1
CGCCG*GGUGAAGCU*CGGCG => 1

Contig2
CAAUC*AUCAA*GAUUG => 1
GAUAU*GU*AUAUC => 1
AAAAU*CCAAUAUUUCCAU*AUUUU => 1