Immediately, what seems to be a bug comes out. 
if (      $genomepair eq 'aa' ) { ++$tt; }

[download]

If it's 'aa', why increment $tt? If it's not a bug, then it needs a comment explaining why it doesn't follow the pattern.

Continuing with the refactoring, once you have it in the second form listed, you can easily move to a hash. 

my %pair_count;

my $genomepair = $genome[$i] . $genome[$i+1];
$pair_count{$genomepair}++;

[download]

------
We are the carpenters and bricklayers of the Information Age.

The idea is a little like C++ templates, except not quite so brain-meltingly complicated. -- TheDamian, Exegesis 6

... strings and arrays will suffice. As they are easily available as native data types in any sane language, ... - blokhead, speaking on evolutionary algorithms

Please remember that I'm crufty and crochety. All opinions are purely mine and all code is untested, unless otherwise specified.

In reply to Re: A less extreme change.. by dragonchild
in thread how can I speed up this perl?? by Anonymous Monk

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