Molecular characterization of full-length SIVcpz proviruses. (A) Individual RT-PCR amplicons (shaded boxes) of SIVcpzUG38, SIVcpzUG31, and SIVcpzTAN5 are shown in relation to the SIVcpz genome (top). All fragments are drawn to scale, with nucleotide sequences numbered starting at the beginning of the R region in the 5′ LTR (see scale bar). (B) Distance plots illustrating the extent of nucleotide sequence divergence between SIVcpzUG38 and SIVcpzUG31 (red), SIVcpzTAN5 (blue), and SIVcpzANT (green). Differences were calculated for windows of 300 bp moved in steps of 20 bp along the alignment; values are plotted at the midpoint of the window. Arrows indicate the start of the gag, pol, vif, vpr, env, and nef reading frames.