Figure 1.

Pair HMMs assuming an affine gap model. Assume two homologous sequences x and y. Let m_i be the ith nucleotide in sequence x and n_j be the jth 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.