Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3869
Accession number HM583629
Name Vin41
Sampling year 2009

HM583629 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:

ctagccctca gatgctgcat ataagcagct gcttttcgcc tgtactgggt ctctctggtt agaccagata -gagcctagga gctctctggc tagctaagga acccactgct taagcctcaa taaagcttgc ctttgagtgc ttcaagtagt gtgtgcccgt ctgttgtttg actctggtaa ctagagatcc ctcagaccac tgaaggcggt ataaaaaatc tctagca

The optimal secondary structure:

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