Figure 2

Conservations and the 22 targeted regions. The position and length of each gene in NL4-3 is shown above the corresponding position in the conservation graph for NL4-3. Conservations were calculated for 8, 846 19 mers from the NL4-3 gene sets against 24.8 million 19 mers in the corresponding HIV-1 variant gene sets, and plotted as conservations for all subtypes, and the clade B only subtypes. The NL4-3 genomic co-ordinates for the starting position of the 22 regions covering the 96 selected targets are given below the conservation graphs. The 22 regions and their component targets (divided into the targets made as hairpins with 20 and 21 bp stems) are shown at the bottom. Region numbers in red are the regions that have overlapping gene targets (e.g. region 1 hairpins include #1, #95 and #96, and target both the LTR and Nef). Regions 1, 2 and 3 within the LTR are repeated in light grey to indicate their overlapping target positions.