I do not know what a k-mer is, so I may get your explanations wrong, but it seems to me that you're only using the diagonal of your matrix. Why don't you extract that diagonal into an array and the search will be easier and faster. Or maybe I did not understand what you are actually doing.

As a side note, this syntax: 

for (my $i =0; $i<6; $i++){

[download]
could be replaced by something more perlish: 
for my $i (0..5) {

[download]

Je suis Charlie.

In reply to Re: Combinatorial problem by Laurent_R
in thread Combinatorial problem by baxy77bax

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