Fig. 9

R5 and X4 LTR sequences demonstrate signature enriched nucleotide variants in transcription factor binding. HIV-1 transcription factors that have been confirmed in vitro, C/EBP-II (HXB2 positions 281–289), ATF-CREB (330–337), C/EBP-I (338–349), NF-κB-II (350–359), NF-κB-I (363–373), Sp-III (377–386), Sp-II (388–398), and Sp-I (399–408), as well as the TAR stem loop (454–518), were evaluated to detect enrichment and depletion of nucleotide variants in R5 and X4 sets of aligned LTR sequences using two sample logos. Enriched nucleotides were plotted proportional to the difference between the populations, with the sum of the most differential position plotted on the vertical axis