If you need a fast and memory efficient solution for your problem, I recommend Bio::Grep. Your matching here 
foreach  $combinations (@motifs){
   foreach $sequence(@file)  {
     if($sequence =~/$combinations/){
      $counter++;
    }
   }

[download]
is slow. Really slow.

Disclaimer: Bio::Grep is written by me ;).

In reply to Re: discovering motifs by lima1
in thread discovering motifs by Anonymous Monk

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