What are the base degeneracy codes that you use (eg. R, W, K, V, S)?
The one letter codes for degenerate bases are determined by the International Union of Biochemistry (IUB), based on base properties. For example, the letter Y is the symbol for unspecified pyrimidine nucleoside and the letter R is for unspecified purine nucleoside. The letters used for ordering degenerate bases are as follows: R = A,G ; Y = C,T; M = A,C ; K = G,T; S =C,G; W = A,T; H = A,C,T ; B = C,G,T ; V = A,C,G ; D = A,G,T; N = A,C,G,T