Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2036
Accession number AY610976
Name 01SP27595
CountrySpain (Equatorial Guinea)
Sampling year 2001

AY610976 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 gctttctgcc tgtactgggt ctctcttgtt agaccagatt tgagcctggg agctctctgg ctagcagggg aacccactgc ttaaagcctc aataaagctt gccttgagtg ccttgagtag tgtgtgcccg tctgttgtgt gactctggta actagagatc cctcagacta ctctaggcgg tgta-aaaatc tctagca

The optimal secondary structure:

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