Figure 1

Pair HMMs assuming an affine gap model. Assume two homologous sequences x and y. Let m _i be the i th nucleotide in sequence x and n _j be the j th nucleotide in sequence y. M represents the state that m _i is aligned to n _j , I _x represents the state that m _i is aligned to a gap (in an insertion with respect to y), and I _y represents the state that n _j is in an insertion with respect to x. The numbers shown after x or y indicate the positions of m _i and n _j in the insertion with respect to the other sequence. The transition probability is shown between states.