Anonymous Monk,
You can check out the pack/unpack tutorial for more information, but here was my logic.

my $pairs = "a2" x ((length $dna)/2);
#  The x operator (perldoc perlop) repeats LHS string times the RHS


$seq{$_}++ for unpack $pairs, $dna;
#  Break string up into a list of 2 char strings
#  Increment the corresponding hash value by 1
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Cheers - L~R