Really beautiful!
Just a question to your %2 part
Is this only for obfusication, or is there a deeper math sense hidden in it 8-).
I guess the print is in :

CG
T--A
A---T
 A----T
  C----G
   T----A
    A---T
     G--C
      CG
      CG
     C--G
    G---C
   G----C
  C----G
A----T
C---G
G--C
  AT
   CG
   A--T

And now I see that there IS a deeper sense :-) Congrat.
Maybe this is the first step to write a perl program which make changes to itselfe and see what's gonna happen. So there is maybe a chance, that this perl program becomes a perl Operating System one day ...
ok, stop dreaming but keep on hoping :)

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