Okay.

sub chain {
    my ($genome,@genome) = @_;
    for ($i..$#genome) {
 ....
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Where is $i set? for $_ ( $i .. $#genome)? and 32 Uninitialised string in eq errors every loop, if the loop had a defined starting place.

sub hash_array {
    my ($genome,@genome) = @_;
    $counts { $genome [$i] . $genome [$i + 1] } ++ for (0..$#genome);
}
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Where does $i come from? <and that's only scratching the surface.

Ah, you're right. I ran it and saw benchmark numbers that looked right, and so I figured it was fine. I'm sorry. However, it would have been courteous to not have been so vague in your first post; I probably would have bothered to re-look at my code.