This looks like a really fun problem to work on, but I'm unclear about your listed possibilities. Could you please (please please please) provide several examples of each of the five listed cases and a test set (maybe 20 or 30 items) with expected results.

In reply to Re: Filtering matches of near-perfect-matched DNA sequence pairs by Anonymous Monk
in thread Filtering matches of near-perfect-matched DNA sequence pairs by onlyIDleft

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