Figure 2.

Zero order HMM using an alphabet of two nucleotides (A,T) for clarity. Circles represent states; arrows represent transitions. The numbers alongside the arrows specify transition probabilities. The emission distribution for each state (except for the silent start state) is contained within each circle. If this were a real zero order model, the four emitting states would contain distributions over all four nucleotides. Adapted from Durbin et al. (8).