Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2064
Accession number AY611005
Name 02SP68963
CountrySpain (Morocco)
Sampling year 2002

AY611005 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 ataagaagct gcttttcgct tgtactgggt ctctctaggt ggaccagatt tgagcctggg agctctctgg ctatctaggg aacccactgc ttaagcctca attaagcttg ccttgagtgc tctaagtagt gtgtgcccat ctgttgtgtg actctggtaa ccagagatct at----------------------aaaatctc ttgca

The optimal secondary structure:

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