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Table 2 Primers for Gag amplification and sequencing

From: The PTAP sequence duplication in HIV-1 subtype C Gag p6 in drug-naive subjects of India and South Africa

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

 
  1. EFP- External forward primer, ERP-External reverse primer, IRP- Internal reverse primer, IFP-Internal forward primer, Reverse primers have been presented as reverse complement