A B Overlapped region MR =　matched bases (40) / total bases of overlapped region (40) = 1 Matched bases = 40 (substitutions and insertion/deletion : 0)

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A B Overlapped region MR =　matched bases (40) / total bases of overlapped region (40) = 1 Matched bases = 40 (substitutions and insertion/deletion : 0) ATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCTTTGGGG ATGGCCGTCATGGCGCCCCGAACCCTCCTCCTGCTACTCT TGCCGGTACATGGCGCCCCGAACCCTCCTCCTGCTACTCTCGGGGG Query: Target: Matched bases = 38 (substitutions and insertion/deletion : 0) MR =　matched bases (38) / total bases of overlapped region (40) = 0.8 Figure S1. Examples of alignment with BLAT. BLAT identifies no substitutions and insertions/deletions in both cases. However, the bottom case have terminal unmatched sequences in the overlapping region. MR can identify this type of unmatched sequences.