The distribution of nucleotide site differences between two finite sequences

A simple method to obtain the distribution of site differences between two randomly chosen cistrons in a finite population is shown. It is assumed that the number of sites and the number of alleles at each site are finite and that no recombination occurs between sites. The mean and variance of the percent difference and the number of site differences between the two sequences are shown to be simple functions of two variables. The differences between a finite-site model an infinite-site model are discussed. The results are applied to the β-globin polymorphism in man.