Without really checking your code in detail, it looks like you want this:

my($a,$c,$g,$t) = (0, 0, 0, 0);
# or
my($a,$c,$g,$t) = (0) x 4;
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Your version:

my($a,$c,$g,$t) = "0";

That initializes $a to "0" and doesn't assign any value to the other variables.