Figure 3.

SVseq2 uses a semi-global alignment algorithm. The gaps "GTTCTAAGCC" and "GAATCACTTGGA" are without penalty. The gap at "TAC" and "T-C" are with penalty 3. The T-A mismatch are scored -1. Other Matches are scored 1 each. Total score is 23.

Zhang et al. BMC Bioinformatics 2012 13(Suppl 6):S6   doi:10.1186/1471-2105-13-S6-S6