Your code returns

xxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
       NNG
          YGY
                    GYG
                                   NNG
xxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
       NNGYGY
                    GYGY
                                   NNG

[download]

whereas I would have expected

xxxxxxNNNGYGYxxxxxxxGYGYNNNxxxxxxxNNNGNNNxxxxxxx
       NNGYGY
                    GYGYNN
                                   NNGNN

[download]

In reply to Re^2: Perl regular expression for amino acid sequence by ikegami
in thread Perl regular expression for amino acid sequence by seaver

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