This is not addressing the problem you were having, rather it is a suggestion for a simpler way of initialising your %genetic_code hash that would save some typing. The glob function can be used to generate combinations of letters. Your hash contains 64 keys which are all possible 3-character combinations of A, C, G and T. These can be generated using glob like this ...

johngg@shiraz:~/perl/Monks > perl -E 'say for glob q{{A,C,G,T}} x 3'
AAA
AAC
AAG
AAT
ACA
ACC
ACG
ACT
...
TGA
TGC
TGG
TGT
TTA
TTC
TTG
TTT
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Arranging the corresponding amino acid letters in an array allows us to map keys (genetic codes) and values (amino acids) shift'ed from the array together to create the hash lookup.

my %genetic_code = do {
   my @amino_acids = qw{
      K N K N T T T T R S R S I I M I
      Q H Q H P P P P R R R R L L L L
      E D E D A A A A G G G G V V V V
      * Y * Y S S S S * C W C L F L F
      };
   map { $_ => shift @amino_acids } glob q{{A,C,G,T}} x 3;
   };
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I hope this is of interest.