Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1416
Accession number AY839827
Name 04LHS6
CountrySouth Korea
Sampling year 2004

AY839827 isolate has foldings of [DIS region] [PBS region] [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:

tgaaccctca gatgctgcat aaaagcagcc gctttctgct tgtactgggt ctctctggtt agaccagatc agagcctggg agctctctgg ctagctaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc ttcaagtagt gtgtgcccat ctgttgtgtg actccggtac ttagactctg gtaactagag atccctcaga ccattttagt cagtgtggaa aatctctagc a

The optimal secondary structure:

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