English: The boxes in yellow are the match states (M). In the M state the probability distribution is the frequency of the amino acids in that position. The row of diamond shaped states are insert states (I) which are used to model highly variable regions in the alignment. The circular states are delete states (D). These are called silent states since they do not match any residues, and they are there merely to make it possible to jump over one or more columns in the alignment.The final probabilistic model conveys the estimation of the observed frequencies of the amino acids in each position, as well as the transitions between the amino acids derived from the observed occupancy of each position in a multiple sequence alignment.^[1]