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. 2016 May 3;13:32. doi: 10.1186/s12977-016-0266-9

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© Antell et al. 2016

Open AccessThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.

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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