I can't see what you are trying to achieve and I don't know what a "fasta sequence" is. Can you give a sample of the output that you would expect?
In the mean time, you probably mext pos ($str) rather than simply pos to manipulate the last capture pos for $str. I suspect also that you don't actually want the lookahead, it should be just a match.
Remember that a look ahead assertion is a 0 width match.
Perl is Huffman encoded by design.
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