Table 2.
Oligonucleotide primers
| Primer | Sequence (5′–3′) | Nucleotide positiona (range) |
|---|---|---|
| 24-kb repeats | ||
| MmmSC_rpoC_fwd | GCGCTGTTGCTATAATTTCTG | 1153795–1153815 |
| MmmSC_IS1296rev1 | CAGGGATTTCATTATCAGCAC | 1154820–1154800; 1178577–1178557; 1202341–1202321b |
| MmmSC_MSC1011rev | CCTACGTTTCCCAGTTTAAGC | 1156846–1156826; 1180603–1180583b |
| MmmSC_1rev | TGATGATGTTTGACAAGAATATG | 1157471–1157449; 1181228–1181206 |
| MmmSC_asnA5′ | CTTGTACTTCACCAATATGAGC | 1157867–1157888; 1181624–1181645 |
| MmmSC_asnA3′ | CAAACTCAACAAGCTATTCAAG | 1158758–1158737; 1182515–1182494 |
| MmmSC_23760fwd | AATAATAATGCAGTTCCACAATC | 1178055–1178077; 1201819–1201841 |
| MmmSC_IS1296rev2 | TGATGCACTGATGTAACAGAG | 1202533–1202513b |
| MmmSC_MSC1061rev | AGAACAGGACCCGTACTATC | 1204456–1204437 |
| 13-kb repeats | ||
| MmmSC_ptsG5′ | GGCATTTGCTGCTAATATTATG | 978849–978870; 994029–994050 |
| MmmSC_ptsG_rev | TGCTAAAGCTACAGAAATACAG | 979077–979056; 994257–994236 |
| MmmSC_ptsG3′ | CAACTTTCATTTCACTTACAGG | 980827–980806; 996007–995986 |
| MmmSC_MSC0861 | TGGATTAAGTTTAGATGTATTAAG | 981581–981604; 996761–996784 |
| MmmSC_glkR | CAAGTGCAGCAGCATTAA | 984475–984458; 997777–997760 |
| MmmSC_arcC3′ | TTTAACAAATTTAGTTCCACTTAG | 985163–985186; 998465–998488 |
| MmmSC_arcC5′ | GTAATTGCAATTGGTGGAAATG | 986080–986059; 1001263–1001242 |
| MmmSC_mgtA2F | CAAAATAATAACCCGCAATTGC | 987867–987888; 1003049–1003070 |
| MmmSC_mgtA2R | GGATTTGCATCATTTTTAGATAC | 988626–988604; 1003807–1003785 |
| MmmSC_mgtA_fwd | GAGTTAATCCAACTGCAACAG | 989253–989273; 1004434–1004454 |
| 12-kb repeats | ||
| MmmSC_patB_F | TGAATAAGTTTAAATCTGAGTTTG | 894982–895005; 910921–910944 |
| MmmSC_patB_R | AGATTTTTAGTTTTTCAACTAATTG | 896154–896130; 912093–912069 |
| 8-kb repeats | ||
| MmmSC_oppFfwd | GGTTAATAAAGTACAAATGATTTTTC | 1104343–1104368; 1112075–1112100; 1121744–1121769 |
| MmmSC_oppFrev | TTCAAATTTATACACTTCTAGTTC | 1105276–1105253; 1113008–1112985; 1122674–1122651b |
| TaqMan | ||
| lppQTM-L | AATAATCAACAAAAAAAAGAGCAAGTAAGTAA | 1166019–1166050; 1189776–1189807 |
| lppQTM_FT | ACATCTTGTTTTTGTCACTCATTTTTTGGTTCAATTTT | 1166113–1166076; 1189870–1189833 |
| lppQTM-R | TAGCCCTTTTATTTTTAGTAATGCTTGTAA | 1166144–1166115; 1189901–1189872 |
| glpOTM-L | CTGAAGCAGGTATTGTAAATTCTGTAGTATT | 294492–294462 |
| glpOTM-FT | CATTCATGGAAAAGGAGTTATTGTTGCTCCAA | 294449–294418 |
| glpOTM-R | AAAGCAGTTGGTCCTACCATAACTCT | 294381–294406 |
a
Based on the nucleotide sequence NC_005364.
b
Primers anneal also to homologous sequences out of the repeats investigated in this study. Only positions in the relative repeats are listed.