I'm not sure how you got those results, and the code you posted had some trouble running too. Apparently the __DATA__ wasn't being imported correctly.

I changed that to a definition:

$cftr="AUGCAGAGGUCGCCUCUGGAAA...";

Everything ran fine after that, except that japhy just spins for a while and then outputs nothing. Otherwise, the results appear to be as expected.

Update: With respect to scain's update, this update basically says that I didn't actually read his update, and so, this entire node is kind of pointless.