01234567890 AAAAAAAAAA AAAAAAAAAAA ========== Offset 0 -- 0 mismatches. 01234567890 AAAAAAAAAA AAAAAAAAAAA ========== Offset 1 -- 0 mismatches. 01234567890 CCAAAAAAAA AAAAAAAAAAA xx======== Offset 0 -- 2 mismatches. 12345678901 CCAAAAAAAA AAAAAAAAAAA xx======== Offset 1 -- 2 mismatches. ## 806 other 2-mismatch matches your code fails to find 12345678901 AAAAAAAATT AAAAAAAAAAA ========xx Offset 0 -- 2 mismatches. 12345678901 AAAAAAAATT AAAAAAAAAAA ========xx Offset 1 -- 2 mismatches.