Table S1 Primers used in this study. The physical location of the primer pairs in the M. tuberculosis H37Rv chromosome is shown in Figure 1
No. of primer / PCR Start
(bp) / PCR Stop
(bp) /

Primer Sequence

/ Genes and intergenic regions amplified
1F /

6457

/

7734

/

5’-TGT GAA CAA GGC TGT GTC CT-3’

/ Rv0005 (gyrB),Rv0005 (gyrB)- Rv0006 (gyrA)a,Rv0006 (gyrA)
1R /

5’-TTT CCC TCA GCA TCT CCA TC-3’

2F /

156439

/

156638

/

5’-CGAGTTAGCTTGGCTTCCAG-3’

/ Rv0128-Rv0129c(fbpC)a,Rv0129c(fbpC)
2R /

5’-TAT CCA GCA TGT GCT CAA CG-3’

3F /

408401

/

409792

/

5’-CGA TGC GTC GTA TGC TTG-3’

/ Rv0339-Rv0340a,Rv0340,Rv0340-Rv0341 (iniB)a,Rv0341 (iniB)
3R /

5’-ATC ACG GCA GTA AAA CCC AG-3’

4F /

409773

/

410222

/

5’-CTG GGT TTT ACT GCC GTG AT-3’

/ Rv0341 (iniB)
4R /

5’-CGA CAG ATG AGG CAT AGC AG-3’

5F /

410771

/

411872

/

5’-GTA CGG CCT TTT CGG ACT AC-3’

/ Rv0341 (iniB)-Rv0342 (iniA)a,Rv0342 (iniA)
5R /

5’-CTC CAA ATC CGAAGC AAG TC-3’

6F /

412271

/

413105

/

5’-CCG GGG CCA TAA AAT GAT TA-3’

/ Rv0342 (iniA),Rv0342 (iniA)-Rv0343 (iniC)a,Rv0343 (iniC)
6R /

5’-GCA GGT CGA AAC TCA GCC-3’

7F /

413413

/

413913

/

5’-CAT CGA CGC GAT GCT CTC-3’

/ Rv0343 (iniC)
7R /

5’-GCA ATG ACG TAC GGG GTC-3’

8F /

760241

/

760753

/

5’-GGT GTT CAT GGG TGA CTT CC-3’

/ Rv0667 (rpoB)
8R /

5’-AGC CCG AGC TTC TTG TTG AC-3’

9F /

760811

/

761918

/

5’-CAT CGA ATA TCT GGT CCG CT-3’

/ Rv0667 (rpoB)
9R /

5’-GTC GTC AGT ACA GGG ACC GT-3’

10F /

781511

/

781940

/

5’-CAT GGC CGA CAA ACA GAA C-3’

/ Rv0681-Rv0682 (rpsL)a,Rv0682 (rpsL)
10R /

5’-GTG GCA TCA GCC CTT CTC T-3’

11F /

1415793

/

1417393

/

5’-GTA GGG CCC AAA CAT CGA G-3’

/ Rv1266c (pknH)-Rv1267c(embR)a,Rv1267c(embR),Rv1267c(embR)-Rv1268ca
11R /

5’-GAC ACC CTA TTG GCA CCT TG-3’

12F /

1471952

/

1473492

/

5’-GGT GAG TAA CAC GTG GGT G-3’

/ Rvnr01 (rrs)
12R /

5’-AGT GTG TTG GTG GCC AAC TT-3’

13F /

1673222

/

1673622

/

5’-GAC ATA CCT GCT GCG CAA T-3’

/ Rv1482c-Rv1483 (mabA)a,Rv1483 (mabA)
13R /

5’-GTC ACA TTC GAC GCC AAA C-3’

14F /

1674176

/

1674906

/

5’-GCC ACT GAC ACA ACA CAA GG-3’

/ Rv1483 (mabA)-Rv1484 (inhA)a,Rv1484 (inhA)
14R /

5’-CGC ATC CTT CAT GTT CCA G-3’

15F /

1792286

/

1792606

/

5’-GGT GTC AGC GCT TGG ATT-3’

/ Rv1591-Rv1592ca,Rv1592c
15R /

5’-GAA CAT GTG TCC CTG CAC C-3’

16F /

1793614

/

1793758

/

5’-CAG GTG GGA AGT AGA ACG GA-3’

/ Rv1592c
16R /

5’-GGC CAT GAA GGG AGC CTA-3’

17F /

1917844

/

1918772

/

5’-CTC TGG CCG AAC TCG AAG-3’

/ Rv1693-Rv1694 (tlyA)a,Rv1694 (tlyA),Rv1694 (tlyA)-Rv1695 (ppnK)a
17R /

5’-CAG CAG AAC ACT GCG ATG AG-3’

18F /

2006275

/

2006830

/

5’-AGA TCA TGG ACG ACT ACG CC-3’

/ Rv1771-Rv1772a,Rv1772
18R /

5’-TAT TTC GAA GAC CGG CAA TC-3’

19F /

2101933

/

2103139

/

5’-CAT CGA TCC CTT GTC GAA GT-3’

/ Rv1854c(ndh),Rv1854c(ndh)-Rv1855ca
19R /

5’-ACA CAT GTC CTC AAC TGG GC-3’

20F /

2153718

/

2155113

/

5’-CTT TCT CCT CAT CCC CGT C-3’

/ Rv1907c-Rv1908c(katG)a,Rv1908c(katG)
20R /

5’-CGA GAT CCT GTA CGG CTA CG-3’

21F /

2154939

/

2156726

/

5’-CTC ATA GAT CGG ATC CAC CC-3’

/ Rv1908c(katG),Rv1908c(katG)-Rv1909c(furA)a,Rv1909c(furA)
21R /

5’-ATC GGA ACA TAC GAA GGC TG-3’

22F /

2288584

/

2289321

/

5’-GTG AAC AAC CCG ACC CAG-3’

/ Rv2042c-Rv2043c(pncA)a,Rv2043c(pncA),Rv2043c(pncA)-Rv2044ca
22R /

5’-GGC GTC ATG GAC CCT ATA TC-3’

23F /

2515043

/

2516429

/

5’-GTT CGG CTT TTC CGA CAC T-3’

/ Rv2241 (aceE)-Rv2242a,Rv2242
23R /

5’-GCA CTG TGT TTG GAT GAA CG-3’

24F /

2517507

/

2517704

/

5’-GTC TCC CAG CTC ACC CAA C-3’

/ Rv2243 (fabD)
24R /

5’-AGT CCG CGG TTA TAG GTT TG-3’

25F /

2518207

/

2519441

/

5’-CAC GTG GAA GGG TCT GTT G-3’

/ Rv2245 (kasA),Rv2245 (kasA)-Rv2246 (kasB)a
25R /

5’-CTT CCA TAT CGG TCC GAC TC-3’

26F /

2521329

/

2521524

/

5’-ACG ACG AAC TCG ATG CCT AC-3’

/ Rv2247 (accD6)
26R /

5’-AAC TCG TCG AAC GGT GTG TC-3’

27F /

2725501

/

2725996

/

5’-CTG GCC AGG TAA GAC GAC C-3’

/ Rv2427c (proA)-Rv2427Ac (oxyR)a,Rv2427Ac (oxyR)
27R /

5’-TTC TCG ATA TGA GC CAG TCG-3’

28F /

2726012

/

2726857

/

5’-TGA ACC ACT GCT TTG CCG-3’

/ Rv2427Ac (oxyR)-Rv2428 (ahpC)a,Rv2428(ahpC)
28R /

5’-TGA TGT CTT TGG CGT ACT CG-3’

29F /

3073614

/

3074026

/

5’-ACA CGC GTC ACT CCT TGA TT-3’

/ Rv2763c (dfrA)-Rv2764c(thyA)a,Rv2764c(thyA)
29R /

5’-TCT TCC AGT TCT ACG TCG CC-3’

30F /

3154172

/

3154632

/

5’-CCA CAC CCT GGG ACA ACC-3’

/ Rv2846c (efpA)
30R /

5’-TAT GAC GGC TCT CAA CGA CA-3’

31F /

3489314

/

3489804

/

5’-TTT CGA TGC TGT TTG TCA GC-3’

/ Rv3123-Rv3124a,Rv3124
31R /

5’-TGC TGT CGA TCT CCA ATG AG-3’

32F /

3505197

/

3505378

/

5’-TAT CAG ATG CCT GGC GTG TA-3’

/ Rv3138 (pflA)-Rv3139 (fadE24)a,Rv3139 (fadE24)
32R /

5’-AGG TGG TGT TGG TCA TAC GG-3’

33F /

3645180

/

3645659

/

5’-CAA CG CAC CGG GAG ATA C-3’

/ Rv3264c(manB)
33R /

5’-ATG GTG TTT AAC GGC GAT GT-3’

34F /

3646565

/

3647921

/

5’-AGT AGT GCA TCG ATA CTG CCC-3’

/ Rv3265c (wbbL)-Rv3266c (rmlD)a,Rv3266c (rmlD),Rv3266c (rmlD)-Rv3267a
34R /

5’-TAC GAA CCG TAC GAA CCA CA-3’

35F /

4007463

/

4008036

/

5’-GGC AAG GCG GAT CTT CTC-3’

/ Rv3566c (nat)
35R /

5’-CGA CGA CCT CAG TCC ACA G-3’

36F /

4239799

/

4241163

/

5’-GTT TCG TCG TCG AGG ACA TT-3’

/ Rv3792,Rv3793 (embC)
36R /

5’-AAG GCA CCG ATG ATG CAG-3’

37F /

4241960

/

4242879

/

5’-CTA GCC GGA ATT GTC CAG TC-3’

/ Rv3793 (embC)
37R /

5’-GTC TCG TCG ACG CCG TAT-3’

38F /

4243088

/

4244363

/

5’-AAC CTA GGA ACG GTG ACT CG-3’

/ Rv3793 (embC)-Rv3794 (embA)a,Rv3794 (embA)
38R /

5’-GTT GTT GAA CGG CAG CCA G-3’

39F /

4244402

/

4246089

/

5’-GGT CAC GTG GGT GTT GGT-3’

/ Rv3794 (embA)
39R /

5’-ATT GCT CAG GGC TCA GGT T-3’

40F /

4246828

/

4248079

/

5’-AGG CAA GGA CGC CAA TTT-3’

/ Rv3795 (embB)
40R /

5’-GTT CTC GGT ATA CCA CGC CT-3’

41F /

4247975

/

4250032

/

5’-GTC ATC CTG ACC GTG GTG TT-3’

/ Rv3795 (embB), Rv3795 (embB)-Rv3796a
41R /

5’-GGC TGA GGA GAC TTT TGT GG-3’

42F /

4325997

/

4326413

/

5’-GCT AAA GCT AAA CCC CCA CC-3’

/ Rv3853 (menG)-Rv3854c(ethA)a,Rv3854c(ethA)
42R /

5’-CGA CTA TCG ACG GAC AAC AA-3’

43F /

4326378

/

4326952

/

5’-TCG TGG TGA TG TCC ACT TGT-3’

/ Rv3854c(ethA)
43R /

5’-CGC TAA GAA CAT CGT CGT GA-3’

44F /

4326933

/

4327504

/

5’-TCA CGA CGA TGT TCT TAG CG-3’

/ Rv3854c(ethA),Rv3854c(ethA)-Rv3855 (ethR)a
44R /

5’-GGC CTC GAC ATT ACG TTG AT-3’

45F /

4407460

/

4408212

/

5’-GAT AGT TGA AGC CTG GCC C-3’

/ Rv3918c (parA)-Rv3919c(gidB)a,Rv3919c(gidB)
45R /

5’-GGA GTG CGT AAT GTC TCC GA-3’

46F /

3861875

/

3862458

/

5’-GCCGCTCCAACACGAACGAT-3’

/

rplM

46R /

5’-CGCCGTTCACGCCTGACCGG-3’

47F /

735466

/

736271

/

5’-AGGGCCAGCTTCGGCCCGCT-3’

/

rplA

47R /

5’-CGACACGCCGTGCGTGCGGG-3’

48F /

802479

/

803419

/

5’-ATGCGGCCTAGCCCGGCGAC-3’

/

rplB

48R /

5’-GCGTGGCATGGTTGGCTAC-3’

49F /

800740

/

801532

/

5’-ACGCGCTCATGCGCATCGAC-3’

/

rplC

49R /

5’-ATAGCGCCGTCGACCTTGCC-3’

50F /

801389

/

802193

/

5’-TCAAGGGTGCGGTTCCTGGC-3’

/

rplD

50R /

5’-AGGATTTCTCCGAGATCACC-3’

51F /

811989

/

812690

/

5’-TCGGCTATCGGGTCGACGAG-3’

/

rplE

51R /

5’-TGTAGGCGCGCACGGCAAAC-3’

52F /

813325

/

814007

/

5’-AGGCAGCTAGACAGGGCGTG-3’

/

rplF

52R /

5’-TTCTTCCGCAGCCGCGTGTG-3’

53F /

748204

/

748882

/

5’-TCGTTCCCGGGTGGTCGCAG-3’

/

rplJ

53R /

5’-CGTCCAGCAGTTCGTCGGTG-3’

54F /

811303

/

811814

/

5’-CCGCGCACGTCAGGGATGGT-3’

/

rplN

54R /

5’-GCAAGACTTTGCCCTTGGCC-3’

55F /

805040

/

805596

/

5’-CGCGGGTGGCGAAGAGGCCG-3’

/

rplP

55R /

5’-TCGCGCAACCGCTCGGCCAG-3’

a intergenic regions.