Okay.

sub chain {
    my ($genome,@genome) = @_;
    for ($i..$#genome) {
 ....
[download]

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);
}
[download]

Where does $i come from? <and that's only scratching the surface.