Amplification primers | ||||
---|---|---|---|---|
Primer Number | Description | Co-ordinates (HXB2) /Length | Sequence (5'–3') | Product length |
Set I | ||||
 N420 | EFP | 683–709, 27 | CTCTCGACGCAGGACTCGGCTTGCTGA | 1712 |
 N1476 | ERP | 2366–2395, 29 | CTATCATTTTTGGTTTCCATYTTCCTGGC | |
 N1356 | IFP | 790–806, 27 | AAGGAGACATATGGGTGCGAGAGCGTC | 1516 |
 N1435 | IRP | 2274–2306, 30 | ATTTGGCCCCCTCGAGTTGAGACAAGRGGTCG | |
Set II | ||||
 N420 | EFP | 683–709, 27 | CTCTCGACGCAGGACTCGGCTTGCTGA | 1832 |
 N1634 | ERP | 2484–2515, 32 | TTTCTTCCAATTATGTTGAYAGGTGTRGGTCC | |
 N1632 | IFP | 777–806, 30 | TAGAAGGCTCGAGATGGGTGCGAGAGCGTC | 1666 |
 N1633 | IRP | 2413–2443, 32 | ATRRGTATTTGATCATAYTGTCTTACTTTGAT | |
Set III | ||||
 N1788 | EFP | 577–604, 29 | GACTCTGGTAACTAGAGATCCCTCAGAC | 2315 |
 N1789 | ERP | 2862–2892, 35 | ATGCATCA/CCCCACATCCAGTACTGTYACTG | |
 N1786 | IFP | 625–647, 28 | ATCTCTAGCAGTGGCGCCCGAACAGGGAC | 2211 |
 N1787 | IRP | 2801–2836, 30 | TGTGGAATTCCTAATTGRACYTCCCARAATCTG | |
Set IV- p6 Gag | ||||
 N2301 | EFP | 1752–1778, 27 | GTTGGTCCAAAATGCGAACCCAGATTG | 1090 |
 N2302 | ERP | 2813–2842, 29 | GGGCCATCCATTCCTGGCTTTAATTTTAC | |
 N2304 | IFP | 1859–1885, 27 | GCCACAAAGCAAGAGTGTTGGCTGAGG | 549 |
 N2305 | IRP | 2382–2408, 27 | ACCTCCAATTCCTCCTATCATTTTTGG | |
Sequencing primers | ||||
 N1619 | Forward Primers | 1040–1056, 17 | GGCCATTGACAGAAGA |  |
 N1620 | 1609–1626, 18 | TTGTATGTAGGATCTGA |  | |
 N1621 | 2092–2107, 16 | TGCCCACACTAATGATG |  | |
 N1812 | 2035–2058, 25 | TGTGGAAAGGAAGGACACCAAATG |  | |
 N1489 | 1302–1326, 25 | TGTTTACAGCATTATCAGAAGGAGC |  | |
 N1622 | Reverse primers | 1835–1818, 18 | GCTGTCATCATYTCTTCT |  |
 N1623 | 1329–1313, 17 | GGTGGCTCCTTCTGATA |  | |
 N1624 | 910–895, 16 | GCTCCCTGCTTGCCCA |  | |
 N1490 | 1826–1849, 24 | CACTCCCTGACATGCTGTCATCAT |  |