Figure 5

ACT nucleotide comparison of var gene repertoires. Concatamers of var gene exon1 sequences were arranged sequentially by Ups type: UpsE, A, C, B2-4, and B1, (colored as indicated) with one genome per horizontal line. The isolate-transcendent var genes var2csa, var1csa and Type 3 var are positioned at the left end of the concatemer. BLASTN was performed with word length set at 90 nucleotides (filter for low complexity removed). The comparisons were viewed in ACT with a window size of 120 nucleotides, at minimum 90% identity to show segments of similarity between var genes. Diagonal bands connecting individual var genes are colored according to percent identity, shown in the scale diagram (inset). Band width corresponds to region of sequence identity. Var names are listed, in order of appearance, in Additional file 4: Table S7.