Use a hash. 
$counts {$genome [$i] . $genome [$i + 1]} ++;

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Note: the line above assumes that you are using separate counters for "aa" and "tt", unlike your own code.

Abigail

In reply to Re: how can I speed up this perl?? by Abigail-II
in thread how can I speed up this perl?? by Anonymous Monk

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