Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2037
Accession number AY610977
Name 02SP68651
Sampling year 2002

AY610977 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 gatgctgcat ataagcagct gcttctcgcc tgtactgggt ctctcttgtt agaccagatt tgagcctggg agctctctgg ctagcagggg aacccactgc ttaagcctca ataaaagctt gccttgagtg ctctaagtag tgtgtgcccg tctgttgtgt gactctggta actagagatc cctcagacca ctctagttgg tgta-aaaatc tctagca

The optimal secondary structure:

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