Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2314
Accession number EU938118
Name 03RU951
Sampling year 2003

EU938118 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 gatgctgctt ataagcagct gcttttcgcc tgt-ctgggtc tctctggtta gaccagatc-g agcctgggag ctctctggct agctagggaa cccactgctt aagcctcaat aaagcttgcc ttgagtgctt taagtagtgt gtgcccgtct gttgtatgac tctggtaact agagatccct cagaccactc taggcggtgt a-aaaatctct agca

The optimal secondary structure:

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