Figure 3.

Sequence and conservation profiles for the 96 targets. The sequences of the 96 targets are shown in their 22 overlapping regions. The label column (left) shows the region number, the target gene, the target co-ordinates (relative to the start of the gene) and the number of shRNAs in each group. The sequence column (right) shows the shRNA # above the first nucleotide of the p0 position. shRNA #s shown in red are target start positions shared by two matched shRNAs; 20 and 21 bp stem shRNAs. The percentage conservations of 19 mer windows in all clades, and clade B subtypes only, are shown as colored-coded circles below the starting position of each 19 mer sequence within the profile sets of 5 overlapping sequences. Total conservations for each region are similarly shown at the end of each region. shRNA #s generally proceed in order, except for #95 and #96, which were selected from the Nef target set but are shown on their overlapping LTR target (region 1). An example was made of shRNA #1 with its p0 and p+-1 and p +-2 position 19 mer sequences indicated in more detail.