The code of Re: string match using with an N in any position matches 'CACGT' against 'CBCGTNNN' ('B' vice 'N').
Agreed. But in the genomic encoding scheme of things, the 'N' means 'aNy'. Whereas 'B' means 'any except A'.
With my very limited understanding, 'N' therefore encompasses 'B' in as much as there is no mention in his post of excluding strings that have an 'A' in the wild-card position. Nor is there any mention in the post of the possibility of "targets"(*) ever contains 'B's in the relevant positions.
In this case, the OP seems satisfied with the solution for his particular problem. I'll leave it up to him to know his data and problem domain.
(*An unusual term in this context -- the wild-cards are usually in the query -- but whatever :)
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