I hope you don't mind if I offer a little advice. If your program is not doing quite what you expected and you think the problem might lie with a particular part of the code but you can't work out why, don't persist in trying to fix the program. Instead, break that code out into a smaller script or one-liner and run it to see if it is doing what you expected, perhaps something like this:-

knoppix@Microknoppix:~$ perl -E '
> $trilet = q{AGT};
> say $trilet;
> $ss02 = substr $trilet, 0, 2;
> say $ss02;
> $ss12 = substr $trilet, 1, 2;
> say $ss12;
> $ss22 = substr $trilet, 2, 2;
> say $ss22;'
AGT
AG
GT
T
knoppix@Microknoppix:~$
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It would immediately become obvious to you from the last line of the output that substr $trilet, 2, 2 is not doing what you expected. That would be the time to explore the documentation and read up on the substr function. This is a far less frustrating approach than trying to work out exactly what has gone wrong in your more complex script.