The underlying model of jpHMM. This model is illustrated using a toy example. It is built from a DNA MSA composed of two subtypes, with the first subtype having three sequences and the second one two sequences. For each match and insert state, a vector of emission probability values for the nucleotides is given. For the sake of clarity, the majority of transitions between the two subtypes is omitted. Moreover, the delete state directly right to the begin state B (from which one can go to each match state) as well as the delete state directly left to the end state E (to which one can go from each match state) were left out. High transition probabilities are represented by fat lines, low probabilities by thin lines, and the jumps between the subtypes by dashed lines. The Viterbi path with regards to the query sequence is colored in blue, i.e., the first two positions of the query are assigned to Subtype 1 and the last two to Subtype 2.