Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1998
Accession number AY610967
Name 03SP100655
CountrySpain (Mozambique)
Sampling year 2003

AY610967 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:

cttaccctca gaatgctgca tataagcagc tgcttttcgc ctgtactggg tctctcttgt tggaccagat a-gagcctggg agctctctgg ctagcaaggg aacccactgc ttaagcctca ataaaagctt gccttgagtg cttcaagtag tgtgtgcccg tctgttgtgt gactctggta actagagatc cctcgaacca cgctcggcgg tgta-aaaatc tctagca

The optimal secondary structure:

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