Control Elements Secondary Structures of HIV-1 genome

General information on HIV-1 isolate

# 1302
Accession number AF196734
Name 94ET78
Sampling year 1994

AF196734 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:

ccaaccctca gatgctgcat ataagcagct gcttttcgct tgtactgggt ctctctaggt agaccagatc tgagcctggg agctctctgg ctaactagga aacccactgc ttaaccctca ataaagcttc ccttaagtcc ttcaagtagt gtgcacccgt ctgttgtgta actctggtaa ctagagatcc ctcaaaccct tt-agtcaggg tggaaaatct ctagaa

The optimal secondary structure:

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