I don't know if will help you, but Dominus's excellent Higher-Order Perl (freely downloadable here) discusses a solution to a problem similar to yours in section 4.3.2 "Genomic Sequence Generator".

In reply to Re: Understanding a script that looks for mismatches to a regex by AnomalousMonk
in thread Understanding a script that looks for mismatches to a regex by onlyIDleft

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