As 2teez points out, some three-letter words do occur more than once and a hash for counts rather than individual scalars is the way to go. You could use the glob function for initialization, saving a lot of fiddly, error-prone typing.

my %threeLtrCts =
   map { $_ => 0 }
   glob q{{A,T,G,C}{A,T,G,C}{A,T,G,C}};
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I hope this is helpful.