Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1344
Accession number AB191658
Name 99ZM1116
Sampling year 1999

AB191658 isolate has foldings of [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:

ccaaccctca gatgctgcat ataagcagct gcttttcgcc tgta-tgggtc tctctaggta gaccagatct gagcctggga gctctctggc taactaggga acccactgct taagcctcaa taaagcttgc cttgagtgct -caagtagtgt gtgcccatct gttgtgtgac tctggtaact agagatccct cagaccattt tggt-agtgcg gaaaatctct agca

The optimal secondary structure:

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