Table 1.

Description of primers used in this assay, with primer set, pool, concentration, sequences of forward and reverse primers in the set, and location of primer relative to SIVmac239 (Accession: M33262)

Primer Set	Pool	Concentration (µM)	FWD sequence	REV sequence	Forward primer reference position	Reverse primer reference position
1	1	40	TCCTGAGTACGGCTGAGTGAAG	CCTTCTTTGTTCTCCAACAGGCT	1115–1137	1475–1498
2	2	30	ATTAG G CTACG ACCCAACG G AA	AATTTCCTCCTCTG CCG CTAGA	1363–1385	1711–1733
3	1	20	ACCTAGTGGTG G AAACAGGAACA	GTCCTTGTTGTGGAGCTGGTTG	1628–1651	1987–2009
4	2	20	CCATCAAG CG G CTATG CAG ATT	GCTGCATCTGTCTGTTCTGCTC	1893–1915	2246–2268
5	1	40	TGGGGTTGCAAAAATGTGTCAGA	GCTTTCTTGGTCCCCTCTGTTG	2114–2137	2476–2498
6	2	20	GCCGGGACAGAAGGCTAGATTA	TTTAG CAG ATCCACAG CTG GGT	2376–2398	2720–2742
7	1	30	AATTTCCCCATG G CTCAAG TG C	TCCTATTCCTCCTACTATTTTTGGGGT	2644–2666	2963–2990
8	2	10	TG G ATACAG GGGCTG ATG ATTCT	CCAACTGACCATCCTTTTCCATCTTT	2881–2904	3249–3275
9	1	20	GTCGCCTTAAAGCCAGGAAAGG	GAGGTATGGAGAAATATGCATCACCT	3135–3157	3465–3491
10	2	10	TAGG AATACCACACCCTG CAGG	CCCTGTCATGTTCCAGGTCTGT	3382–3404	3708–3730
11	1	40	ACATG TG CTAG AACCCTTCAG G A	CAG TCCACTG AACTTCCTCTG TT	3602–3625	3996–4019
12	2	10	AGAGAGACCTGGACAGTG AATG A	TG TG CTAATAGTCTCACTCCATTG G T	3852–3875	4213–4239
13	1	40	GAGTCAGGACAATCAGTGGTCTTAT	ATCCTGCTTTCCCTTCTTTTGACTG	4100–4125	4473–4498
14	2	10	TCTCAACACCACCGCTAGTAAGA	TACCTTTGTGTGCTGGTACCCA	4354–4377	4728–4750
15	1	15	CCTACAG AATCAG AGAGCAGGCT	ATTTG CCTG CCCATGTATAG CC	4632–4655	4949–4971
16	2	15	CCCAG AATAGTG GCCAGACAGA	CAAAG G TG TG CTCTATCCCTG C	4869–4891	5202–5224
17	1	30	ATGGTG CTAACTTTG CTTCG CA	GGTCCCTTCCACAGTTGATCTCT	5134–5156	5497–5520
18	2	30	AGGGG ATATG ACTCCAGCAG AA	CCATCCG ACCTTAAAATG GGGC	5357–5379	5742–5764
19	1	25	AG AGGTGG ATAG CAGTTCCCAC	CTTCTCCCG CTG TAAAG CAAG G	5609–5631	5959–5981
20	2	50	GGACAGATGTAACACCAAACTATGCA	TTCCCAAG ACCTTTG CCAAACC	5885–5911	6229–6251
21	1	70	GGAGAAGAGACAATAGGAGAGGCC	CATCCCATGGTTCCCTTTGTGG	6107–6131	6458–6480
22	2	10	TCCCCCTCCAG G ACTAG CATAA	TG CTTCTAG AGGGCGG TATAG C	6385–6407	6704–6726
23	1	30	TCATG CATTTCAG AGGCGG ATG	GCATTCCTCCAAGCTGGTACAC	6615–6637	6972–6994
24	2	10	TTGGG AATCAG CTG CTTATCG C	TGTCAATCCCCATCTATCTGTCTCA	6870–6892	7231–7256
25	1	25	AG TCACAG AACAGG CAATAG AGGA	TCCCTTGTTCACATACCAAATCTGC	7102–7126	7451–7476
26	2	40	AG CTGTAAATTCAACATGACAG GGTT	GTCCTATTATCCCTACCATGCCAGT	7358–7384	7749–7774
27	1	20	GGTGGTCTCTTCATGCACAAGG	TGGGATGTTTGACAATGGTCTGC	7633–7655	7955–7978
28	2	20	AAAGCAGGCATGGTGTTGGTTT	TGGAGTTACACGTGAGGTCTCC	7876–7898	8243–8265
29	1	20	CCAG AAG CCAAAG GAACAG CAT	TTGCGAGAAAACCCAAGAACCC	8113–8135	8471–8493
30	2	20	AG ATG TG AAG AG GTACACTACTG G T	CTAAACGCACATCCCCAAGCAT	8389–8414	8700–8722
31	1	15	TAG G GTCACTG CCATCG AG AAG	TCCAAGAAGCAAGGTCAAACCA	8632–8654	8921–8943
32	2	40	AGCTGGG ATG TGTTTGG CAATT	GCCAAGTCAAGAGGCGTATCAG	8879–8901	9206–9228
33	1	100	GGCAAAGAAAGAGACGGTGGAG	AAGAGAGTGAGCTCAAGCCCTT	9101–9123	9495–9517
34	2	40	CTGGAGATCTGCG ACAG AGACT	GTAATAAATCCCTTCCAGTCCCCC	9370–9392	9734–9758
35	1	40	TTGGTAG G G GTATCAGTG AGGC	CCATGCTAGAACCTCTCCCCAA	9621–9643	9971–9993
36	2	40	CAGATGAGGCACAGGAGG ATG A	ACATCAAGAAAGTGGGCGTTCC	9880–9902	10,205–10,227
37	1	40	AGGG ACTTTCCACAAG GGG ATG	TCGGTTTCCCAAAGCAGAAAGG	10,131–10,153	10,516–10,538