Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1288
Accession number AF196717
Name 97TH62
Sampling year 1997

AF196717 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:

cgagccctca gatgctgcat ataagcagct gctttt-gcct gtactgggtc tctctggtta gaccagatca gagccnggga gctctctggc tagctaggga acccactgct taagcctcaa taaagcttgc cttgagtgca acaagtagtg tgtgcccgtc tgttgtgtga ctctggtaac tagagatccc tcagacacct ttagtcagtg tggaaaatct ctagca

The optimal secondary structure:

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