Figure 2.
A, The substitution matrix that models the neutral evolution rate of nucleotides. The (i,j) entry, Sij in S, represents the probability that the i-th type of nucleotides in C. reinhardtii corresponds to the j-th type of nucleotides in V. carteri, and i and j are one of the four types of nucleotides and are in the order A, C, G, and T. B, Three 8-mer pairs as examples to illustrate that smaller conservation P values are not always corresponding to smaller mismatch numbers. [See online article for color version of this figure.]