When comparing many strings against many strings (not just two), performance actually might matter.

On my machine, your substr method takes 2.65 secs, while the XOR method I suggested above takes only 0.12 secs (for the same data), i.e. it's roughly 20 times as fast.

In reply to Re^2: mismatching characters in dna sequence by Eliya
in thread mismatching characters in dna sequence by prbndr

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