Nope, the dashes are to help the reader understand where there is a is an insertion/deletion (indel) event, and not a substitution of a letter.

Such a gap caused by indel(s). i.e. absence of an aligned letter is commonly signified by the '-' symbol in sequence alignments by biologists.

You may replace it in your mind with just a blank space if that helps you. Hope that clarifies it.

In reply to Re^4: Filtering matches of near-perfect-matched DNA sequence pairs by onlyIDleft
in thread Filtering matches of near-perfect-matched DNA sequence pairs by onlyIDleft

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