Consider a nucleotide x in a region of type r in S 1 with degeneracy-type array t. Then our factors will be given by where with F determined as explained above. We thus are able to construct an emission matrix E, where E(r, t1, t2, t3, x, y) is the probability of in region r, nucleotide x of type [t 1 , t 2 , t 3 ] mutating into nucleotide y.