Your while loop is an infinite loop because you never increment the $counter variable inside the loop.
See also Basic debugging checklist
UPDATE:
I would appreciate ALL the help you have.
You can use qw to cut down on some typing:
my @AAMatrix = qw( A C D E F G H I K L M N P Q R S T V W Y );
You can use map and Range Operators to cut down on some more typing:
my @AAOcc = map { 0 } 1 .. 20;
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