A pair-HMM for pairwise sequence alignment. A pair-HMM is used for alignment of loop regions and calculation of the posterior probabilities in score function. The state M has emission probability distribution for emitting an aligned pair x
. The state I
has distributions for emitting symbol x
against a gap. The state I
has distributions for emitting symbol y
against a gap. The parameters δ and ε are the state transition probabilities.