Pair HMMs assuming an affine gap model. Assume two homologous sequences x and y. Let mi be the ith nucleotide in sequence x and nj be the jth nucleotide in sequence y. M represents the state that mi is aligned to nj, Ix represents the state that mi is aligned to a gap (in an insertion with respect to y), and Iy represents the state that nj is in an insertion with respect to x. The numbers shown after x or y indicate the positions of mi and nj in the insertion with respect to the other sequence. The transition probability is shown between states.
Wang et al. BMC Bioinformatics 2006 7:292 doi:10.1186/1471-2105-7-292