In order to compare our experimentally determined breakpoint distribution to that found in recombinants from the HIV Sequence database, a higher-resolution view of the breakpoint distribution within the env gene was determined using the positions of 133 unambiguously unique recombination breakpoints detectable within 230 env sequences. Following the same procedure described above, but using a 50 nucleotides window to enable detection of breakpoint clusters at the same resolution as in our experimental system, we identified a series of recombination hot-and coldregions within the gene ( Figure 5A , purple graph). In a similar way to the breakpoint distribution detected in cell culture, various hot regions could be defined (light-purple boxes at the bottom of Figure 5A ), which corresponded remarkably well to recombination hot regions 1, 5 and 6 seen in cell culture (light-blue boxes). Whereas the other hot regions identified in cell culture had no corresponding counterparts in the natural breakpoint distribution, there was close correspondence between the cold-spots detected in both distributions.