Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 729
Accession number AB220946
Name 93TH060
Sampling year 1993

AB220946 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:

ctaaccctca gatgctgcat aaaagcagcc gcttttcgct tgtacgtggt ctctcttgtt agaccaggtc -gagcccggga gctctctggc tagcaaggga acccactgct taaagcctca ataaagcttg ccttgagtgc ttaaagtggt gtgtgcccgt ctgtgttagg actctggtaa ctagagatcc ctcagaccac tctagactga gta-aaaatct ctagca

The optimal secondary structure:

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