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Maximum-likelihood phylogenetic trees for intact HIV-1 proviruses from study participants #6, #9, #10, and #12 obtained at days 0 and 28. Coordinates of chromosomal integration sites obtained by integration site loop amplification (ISLA) and corresponding gene names (where applicable) are indicated. Colors denote members of the same clone. $, integration sites that could not be definitively mapped to one exact genomic location due to positioning in repetitive centromeric satellite DNA present in multiple regions of the human genome. See alsoFigure S3.

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