CESSHIV-1 database

General information on HIV-1 isolate

# 1349

Accession number	AF413961
Name	98UA0116 clone 6-ltr
Subtype	A1
Country	Ukraine
Sampling year	2000
Patient	UA0116

AF413961 isolate has foldings of [PBS region] [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 PBS domain

The primary sequence:

tgttgtatga ctctggcaac tagagatccc tcagaccact ctaggcggtg ta-aaaatctc tagcagtggc gcccgaacag ggactcgaaa gcgaaagtt---c cagagaagtt ctctcgacgc aggac

The optimal secondary structure:

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