Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3177
Accession number EF370253
Name 02CWS12c_2695s
CountrySouth Korea
Sampling year 2002

EF370253 isolate has foldings of [123nt 3' terminus] [USE domain, TAR, polyA] [USE region] [227nt 3' terminus] [USE, TAR, polyA] .

The region encompassing 227 nt 3' terminus

The primary sequence:

cgaaccctca gatgctgcat aaaagcagcc gctttttgcc tgtactgggt ctctctggtt agaccagatc cgagcctggg agctctctgg ctgactaggg aacccactgc ttaagcctca ataaagcttg ccttgagtgc tttaagtagt gtgtgaagg-------------------------a gccaccccac aagatttaaa -caccatgcta aaca-----ca

The optimal secondary structure:

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