Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2053
Accession number AY610992
Name 99SP13276
CountrySpain (Equatorial Guinea)
Sampling year 1999

AY610992 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 gaagctgcat ataagcagcc gcttctcgcc tgtactgggt ctcttttgct agaccagatt tgagcctggg agctctctga ctagcagaag aacccactgc ttaagcctca ataaagcttg ccttgagtgc tttaagtagt gtgtgcccgt ctgttgcgtg actctggtat ctagagatcc ctcagaccac tctagactgt gta-aaaatct ctagca

The optimal secondary structure:

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