Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2087
Accession number AF196749
Name 95LB11
Sampling year 1995

AF196749 isolate has foldings of [Core poly(A) site] [123nt 3' terminus] [USE domain, TAR, polyA] [USE region] [227nt 3' terminus] [Complete poly(A) region] [USE, TAR, polyA] .

The region encompassing 227 nt 3' terminus

The primary sequence:

ctaaccctca gaagctgcat ataagcagcc g-ttttcgcct gtactgggtc tctcttgttg gaccagattt gagcctggga gctctctggc tagcaaggga acc-actgctt aaagcctcaa taaagcttgc ctaagttgct tcaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagaccact ctagacagta ta-aaaatctc tagca

The optimal secondary structure:

The suboptimal structures within ΔΔG ≤ 4 kcal/mole of the minimum free energy