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Finite state automaton representing the scoring of pairwise alignments. The three states correspond to the relative phases of the sequences. Insertions and deletions with z ≠ 0 lead to local changes in-phase that are penalized by Ω. Extension in each of the two out-of-frame states S+ and S− is penalized by ω. In/dels interpreted as sequencing errors or true frameshifts are penalized by Δ.
