Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 3874
Accession number HM583634
Name Vin58
Sampling year 2009

HM583634 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 gcttttcgcc tgtactaggt ctctctggtt agaccagatc -gagcctagga gctctctggc tagctaagga acccactgct taagcctcaa taaagcttgc cttaagtgct ttaagtagtg tgtgcccgtc tgttgtatga ctctagtaac tagagatccc tcagaccatt ctaggcggtg ta-aaaatctc tagca

The optimal secondary structure:

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