. 2007 Mar 14;45(5):1483–1490. doi: 10.1128/JCM.02191-06

TABLE 1.

Primer sequences

Primer set	Primer name^e	Sequence (5′ to 3′)	T_m^f (°C)
Internal control	Internal control	TCC CAG TGA CGT TGC CTT C	62
	Internal control	GAG CAG CAG TGG AAT TTC GC	62
Universal forward	Universal forward	TTC AAC CAT CGC CGC CTC TAC	62
1	IS21-1 (1262963^a)	GTC GCC GGA GTT GAA GAA GCT GAA CC	62
2	IS21-2 (absent^a)	CGA TCA ATG TTC CGC CTA ATT GAA CC	62
3	IS21-3 (3797825^a)	AAT GCA GAC GAC GCG ACG ATT GAA CC	62
4	IS21-4 (1592^a)	CAG CGA CAC TCA CAG CCA ATT GAA CC	62
5	IS21-5 (1543972^a)	CTG CAC CGC GCG CAA CGA GGT GAA CC	62
6	IS21-6 (2263627^a)	TCC AGG CAC CAG CAT CAA GGT GAA CC	62
7	IS21-7 (2038898^a)	CGT TTG TGG GTG TCC GGT ATT GAA CC	62
8	IS21-8 (2367677)^a	TGT CGC CAG TTA CGC ACG AGT GAA CC	62
9	IS21-9 (3549199^a)	CGC GGA GCC GTC GGC CGC GGT GAA CC	62
10	IS21-10 (888990^a)	TGA GGG GGT GTT GAG GTT GGT GAA CC	62
11	IS21-11 (3379025^a)	GGG TTT TAA AAA AGT CGC TGT GAA CC	62
12	IS21-12 (3127932^a)	GAT GGC ACG GCC GAC CTG AAT GAA CC	62
13	IS21-13 (3547342^a)	GAC CGC GGT TGG GTG GAC ATT GAA CC	62
14	IS21-14 (3378553^a)	CCC GCG CCT GCG CAA TTG GCT GAA CC	62
15	IS21-15 (3844681^a)	GCG ATG TGG ATT GTG TCG GGT GAA CC	62
16	IS21-16 (1986638^a)	ATC TGT TCA TCT CCG ACC TGT GAA CC	62
17	IS21-17 (absent^a)	CGC GCG GTT CGA ATA CGG TGT GAA CCC	62
18	IS21-18 (2163649^a)	TAC CAG CGA CGT TAA ACG GAT GAA CC	62
19	IS21-19 (3493910^a)	GAA CCC CGG CTC CGC CTC GAT GAA CC	62
20	IS21-20 (1657015^a)	GAG GCT CCT TTC GAC CGC GTT GAA CC	62
21	IS21-21 (2366892^a)	GCG TGA TGT GCA CCA TAG TGT GAA CC	62
22	IS21-22 (2634022^a)	GGT GCG GGG TCG GGG CCG TTT GAA CC	62
23	mutT2 (codon 58)^b wt F	AGA GCT CGC CGA AGA ACC GG	70
	mutT2 (codon 58^b) mut F	AGA GCT CGC CGA AGA ACC GC	70
	mutT2 (codon 58^b) R	AAG CAG ATG CAC GCG ATA GG	70
24	mutT4 (codon 48^b) F	AGC CGA GAA TCA CAT GGA CG	68
	mutT4 (codon 48^b) wt R	CGA GGT GAG CGG GAT CG	68
	mutT4 (codon 48^b) mut R	CGA GGT GAG CGG GAT CC	68
25	ogt (codon 12^b) F	CCG CAG GAG AAG ATC GCA T	68
	ogt (codon 12^b) wt R	GCC CGG CCA GGG TTA ATA GC	68
	ogt (codon 12^b) mut R	GCC CGG CCA GGG TTA ATA GT	68
26	ogt (codon 37^b) F	CCA TCG GGC CAT TAA CCC T	66
	ogt (codon 37^b) wt R	TCG GGT GTC CAG TGT GCG C	66
	ogt (codon 37^b) mut R	TCG GGT GTC CAG TGT GCG A	66
27	RD105^c F	ACA GCG CGG GTC ATA TCA C	62
	RD105^c int	GCA ACA CCC GCT TGT CTT TG	62
	RD105^c R	AAC CAG CTC CTC GAC GCT ATC	62
28	RD142^c F	CCG GTG GTA CGG GTA TTT CC	62
	RD142^c int	GCT CGA GCA TGA TCA GCA AAG	62
	RD142^c R	TAG CAC CAG TAC CGG ATG TCC	62
29	RD150^c F	AGT GCT GGC AAT AGC GGT TG	62
	RD150^c int	CAC CGG CAC TTA CCA TCT CG	62
	RD150^c R	CCA GCA CTT GTT GCA ACT TCG	62
30	RD181^c F	AAA TCC GCC CAT ACC CGT C	62
	RD181^c R	AGC TTC GAC TGG CCA TAG GC	62
31	797736^d wt F	CAG CTC ATC TGT TGA TGT TC	66
	797736^d mut F	CAG CTC ATC TGT TGA TGT TT	66
	797736^d R	ACG CCA TAA GCA CCT TCA CAC	66
32	909166^d wt F	CAC GTT TGA CCG GAT CCC GC	69
	909166^d mut F	CAC GTT TGA CCG GAT CCC GT	69
	909166^d R	CGT CCC AAG GAG CAG TCA AG	69
33	1477596^d wt F	GCC CGG CCA GGG TTA ATA GC	69
	1477596^d mut F	GCC CGG CCA GGG TTA ATA GT	69
	1477596^d R	CCG GTA AAC CAA TGG CCA C	69
34	1548149^d F	CGA CGT GAC ATG GCT GGA TT	68
	1548149^d wt R	CCG ACA ACG TCA GCG ATA CC	68
	1548149^d mut R	CCG ACA ACG TCA GCG ATA CT	68
35	1692069^d F	CGA CCC GTG ATC GCA TGT A	69
	1692069^d wt R	CAC CGA GCT CAC CGG CCT TT	69
	1692069^d mut R	CAC CGA GCT CAC CGG CCT TC	69
36	1892017^d wt F	CCA CGT TTC TTG ATG CCT AT	66
	1892017^d mut F	CCA CGT TTC TTG ATG CCT AC	66
	1892017^d R	TAT CGA GGC CGA CGA AAG G	66
37	2376135^d wt F	GTT GAT GTA TAT CGC GGA CA	66
	2376135^d mut F	GTT GAT GTA TAT CGC GGA CG	66
	2376135^d R	GCC GCC GAA TTA GAA CAG C	66
38	2532616^d F	CTG CTT CGA CAC CTT TAA CGC	72
	2532616^d wt R	ATG CCC AAC GCC GCA GTG GGC	72
	2532616^d mut R	ATG CCC AAC GCC GCA GTG GGT	72
39	2825581^d wt F	TGA CGG TCG GAT TCT TGG GT	68
	2825581^d mut F	TGA CGG TCG GAT TCT TGG GG	68
	2825581^d R	AGC CCA CGA GAT ACT GAG CG	68
40	4137829^d wt F	AGA TGG CCT ACC GGA TCA CC	69
	4137829^d mut F	AGA TGG CCT ACC GGA TCA CT	69
	4137829^d R	GAC GCA GTC GCA ACA GTT CAC	69

Chromosomal position of IS6110 insertion site (2).

Codon position of SNP in the mismatch repair gene (15).

RD (19).

Chromosomal position of sSNP (9).

F, forward primer; R, reverse primer; int, internal primer; wt, wild type; mut, mutant.

T_m, annealing temperature.