The regions of the envelope gene that were studied were chosen so as to obtain 700 to 1,500 nucleotides overlapping windows, spanning the whole of env. For each of seventeen different combinations of parental sequence pairs (Figure 2A) , a recombination rate per nucleotide and per reverse transcription run was calculated within a 50 nucleotides sliding window (with 10 nucleotides step size). These were plotted as a function of the location of the window along the gene. To evaluate whether recombination-prone regions exist within the population, data from the 17 different pairs of parental sequences were pooled and an average recombination rate was computed for the different regions, and plotted as function of the position along the env gene ( Figure 2B , top panel). Peaks and troughs were apparent all along the gene, with regions refractory to recombination being more