Its not clear to me if it would help or not, but you may want to look at Algorithm Showdown: Fuzzy Matching which has some high speed solutions for doing this type of problem, albeit for finding all of the fuzzy matches of a list of a words of the same length in gene strings. Warning: some of the discussion in that thread is somewhat acrimonious.

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$world=~s/war/peace/g

In reply to Re: Tell whether two strings differ at only one position by demerphq
in thread Tell whether two strings differ at only one position by rg0now

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