Figure 4.

Part of a profile HMM model. For a profile HMM we depict the transition probabilities associated with the states of a given consensus position in the profile: Match (M), Insert (I), and Delete (D). The three states corresponding to the next position in the profile are referred to with primes. The Match state has three transitions (into I, M', and D'), while the Insert and Delete states have two transitions each (into I and M', and into D' and M' respectively).