 The probability of emitting a particular residue is determined largely by the frequency at which that residue has been observed in that column of the alignment, but also incorporates prior information on patterns of residues that tend to co-occur in the same columns of sequence alignments.This string of match states emitting amino acids at particular frequencies are analogous to position specific score matrices or weight matrices.A profile HMM takes this modelling of sequence alignments further by modelling insertions and deletions, using I and D states, respectively.