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Expansion of W5(i, k) to account for domain insertions. (A) represents the recursion in the original Dynalign algorithm where W5(i, k) considers a conserved domain. (B) and (C) Represent the consideration of an inserted domain in W5(i, k) at two positions: (B) 3′ side of sequence 1 and (C) the 3′ side of sequence 2.
