Measurement of recombination and mutation rates. (Top) Alignment of GAG1 region of HIV-1 WT sequence (pDRNL(AD8)) (top line) and corresponding marker sequence (bottom line) showing the 15 silent mutations introduced into adjacent codons. This created 14 intervals spaced approximately 50 nucleotides apart (range 18 to 156 nucleotides). Numbering is based on the pDRNL(AD8) WT sequence. Dots indicate identical sequence and silent mutations are indicated with orange highlight. (Bottom) Schematic representation of the marker system depicting silent markers (red) and positions of the overlapping amplicons (brown bars) that enable detection of recombination events (Adapted from .