Having defined a pattern of recombination in the absence of selection and the approximate probabilities of recombination events in various parts of env yielding fully functional products, we were interested in determining whether our experimental data could explain breakpoint patterns observed in circulating recombinants. The distribution along the whole HIV genome of 691 recombination breakpoints within HIV-1 group M full genome sequences from the LANL HIV Sequence Databases (http://hiv-web.lanl. gov/) was inferred. The same approach used in Figure 2B to define the probability that at any region of the genome the breakpoints were more clustered than would be expected by chance was used, with a 200 nucleotides window. A previous analysis of HIV recombinants modelled the distribution of breakpoints and indicated a significant clustering of breakpoints in the 59 and 39 ends of the envelope gene and a lack of breakpoints between these regions [32] . Our new analysis (Figure 4 ) confirmed the propensity for breakpoints to be located at the 59 and 39 ends of the env gene and the lack of breakpoints in the majority of its internal regions in recombinants from the database.