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Bootscan analysis of the three Singapore isolates. The subtype reference strains used were Subtype B, HXB2 (black), CRF01_AE, CM240 (light gray), and subtype C, C2220 (gray). A genome alignment of 8701 nts in length, based on HXB2, was used following end trimming. The bootscan window was 350 bp with a step of 50 bp. The recombinant gene mosaic structure is shown at the bottom of the figure with nucleotide positions corresponding to the reference HXB2 sequence.
