Gap penalties in the SP score This figure shows a multiple alignment of three sequences s, t and u. The SP score is the sum over all pairs of sequences of their pairwise alignment score. The contribution to the SP score from the pair (s, t) is computed by discarding columns in which both sequences have indels (arrows). Such indels are said to be external with respect to the pair. Gaps in the remaining columns (gray background) are assessed affine penalties g + λe where g is the per-gap penalty, λ is the gap length, and e is the gap extension penalty.