Identification of recombinant sequences in the genome of EV-71 subgenotype C4 and CV-A16 Tainan 5079. The organization of the EV-71 genome, the respective crossover breakpoints and potential parental sequences are shown. The upper panel shows results of a pairwise comparison between SHZH98 (a), SHZH03 (b) and CV-A16 Tainan 5079 (c) genome sequences against the consensus sequences of EV-71 genotypes A, B2, B4, C2, and CV-A16/G10. The lower panel shows results from the bootscan analysis which illustrates the likelihood of clustering of the putative recombinants with respect to the parental virus. A window size of 400 nucleotides in increments of 20 nucleotides at a time was used. Positions containing gaps were excluded from the comparison.