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. 2015 Apr 9;12:55. doi: 10.1186/s12985-015-0280-x

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© Waugh et al.; licensee BioMed Central. 2015

This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly credited. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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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 [20].