The arrays contain data similar to this:
@truncated_sequences = qw(JFADLKGJLFLGJGAFDJ DSJLJFLDJSLF...E.T.C);
@triamino_combo = qw(AAA AAB AAC AAD.......e.t.c);

$tri_freq{$_} = 0 for @triamino_combo; # <==== NOTE

foreach $prot_string (@truncated_sequences) {
    foreach $tri_seq (@triamino_combo) {
        while ($prot_string =~ /$tri_seq/g) {
            $tri_freq{$tri_seq}++;
            }
    }
}
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