Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2086
Accession number AF196739
Name 89UG57
Sampling year 1989

AF196739 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 gatg-tgcata taagcagctg cttttcgctt gtactgggtc tctcttgtta gaccagatc-g agcctgggag ctctctggct agctagggaa cc-actgctta agcctcaata aagcttgcct taagtgcttc aagtagtgtg tgcccgtctg ttgtgtgact ctggtaacta gagatccctc agacctcttt agtcagtgtg gaaaatctct agca

The optimal secondary structure:

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