FIG. 2.

Locations of recombination breakpoints on HIV-1 env RNA structures. (A) Recombination rates per nucleotide (43) plotted on the structure of the HIV-1 NL4-3 env gene (47). Nucleotides are numbered relative to the HXB2 proviral DNA sequence. Two previously characterized RNA structures, the RRE and the previously identified hairpin in C2, are labeled. (B) Distribution of 371 experimental recombination breakpoints obtained in the absence of selection relative to hairpin RNA structural elements in env (black bars) versus randomly generated breakpoints (white bars) (error bars indicate standard deviations). Breakpoints falling outside hairpin structures are shown both binned by distance from the nearest hairpin and summed.