Scores were generated by calculating the probability of observing the same genotype by chance over a moving 40-kbp window (with the probability of observing the same genotype for any one SFP by chance placed at 0.33). The plot shows the ratio between the probability and the maximum possible probability for regions with at least four SFPs, with 1 indicating the best possible score. The position of antigenic variation clusters (vars, stevors, or rifins), are shown in blue and are marked. SFPs mapping to these genes were excluded from the calculations because our data indicate that mitotic recombination may be occurring in these genes. pfcrt, which is located between bases 307,926 and 311,020 on Chromosome 7, is shown as a black triangle. The trough at pfcrt is likely to be due to the strong selective pressure on pfcrt, and is consistent with the observation that FCB and Dd2 have different alleles of pfcrt even though published SNP data also shows disequilibrium in surrounding regions []. Data for other chromosomes are shown in .