Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 2309
Accession number EU938113
Name 98RU340
Sampling year 1998

EU938113 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 ctctctgggt agaccagatc -gagcctggga gctctctggc tagctaagga acccactgct taagcctcaa taaagcttgg cttgagtggt ttaagtagtg ggtgcccgtc tgttgtatga ctctggtaac tagagatccc tcagaccact ctaggcagtg ta-aaaatctc tagca

The optimal secondary structure:

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