TABLE 2.
Primers and probes used in this study
| Target | Primer or probe | Species | Nucleotide sequence | Position (nt) | Reference |
|---|---|---|---|---|---|
| rrf-rrl intergenic spacer region | 5S(rrf)F | B. burgdorferi sensu lato | CTGCGAGTTCGCGGGAGA | 229-246 | 47 |
| 23S(rrl)R | B. burgdorferi sensu lato | TCCTAGGCATTCACCATA | 482-465 | 47 | |
| Sl | B. burgdorferi sensu lato | CTTTGACCATATTTTTATCTTCCA | 453-430 | 51 | |
| Ss | B. burgdorferi sensu stricto | AACACCAATATTTAAAAAACATAA | 322-299 | 51 | |
| Ga | B. garinii | AACATGAACATCTAAAAACATAAA | 322-298 | 51 | |
| Af | B. afzelii | AACATTTAAAAAATAAATTCAAGG | 305-278 | 51 | |
| VS116 | B. valaisiana | CATTAAAAAAATATAAAAAATAAATTTAAGG | 305-278 | 51 | |
| rrs | 16SMF | B. burgdorferi sensu lato | AGAGTTTGATCCTGGCTTAG | 1529-1510 | 13 |
| 16SMR | B. burgdorferi sensu lato | CCTCCCTTACGGGTTAGAA | 84-103 | 13 | |
| fD3 | B. burgdorferi sensu lato | AGAGTTTGATCCTGGCTTAG | 8-27 | 20 | |
| T50 | B. burgdorferi sensu lato | GTTACGACTTCACCCTCCT | 1497-1479 | 20 | |
| S5 | B. burgdorferi sensu lato | GAGGAATAAGCTTTGTAGGA | 442-462 | 20 | |
| RS11 | B. burgdorferi sensu lato | CTTAACCCAACACCTCACAGC | 1086-1066 | 20 | |
| fla | Fla outF | B. burgdorferi sensu lato | AARGAATTGGCAGTTCAATC | 271-290 | 8 |
| Fla outR | B. burgdorferi sensu lato | GCATTTTCWATTTTAGCAAGTGATG | 767-743 | 8 | |
| PROBE | B. burgdorferi sensu lato | CACATATTCAGATGCAGACA | 300-319 | 59 | |
| BbslSD | B. burgdorferi sensu lato | GCTGTAAATATTTATGCAGCTAATGTTGC | 556-584 | 15 | |
| FL 8 | B. burgdorferi sensu stricto | CTCTGGTGAGGGAGCTCAAACTGCTCAGGATGCACCGGTTCAAGAGGGT | 594-642 | 45 | |
| FL 15 | B. garinii | CTCTGGTGAAGGAGCTCAGGCTGCTCAGACTGCACCTGTTCAAGAAGG | 594-641 | 45 | |
| FL 16 | B. afzelii | TGCTGGTGAGGGAGCTCAAGCTGCTCAGGCTGCACCTGTTCAAGAGGGTGCT | 594-644 | 45 | |
| BbssSD | B. burgdorferi sensu stricto | GGTTCAAGAGGGTGTTCAACAGG | 630-652 | 15 | |
| BgSD | B. garinii | AGGAGCTCAGGCTGCTCAGA | 603-622 | 15 | |
| BafSD | B. afzelii | CTCAAGAAGAAGGAGCTCAGCAA | 644-666 | 15 | |
| BjSD | B. japonica | GCCTGTTCAAGAAGGCATTCAACAG | 627-651 | 15 | |
| BandSD | B. andersonii | TGTTCAAGAGGGTATTCAACAG | 630-651 | 15 | |
| BvSD | B. valaisiana | ACACCTGTTGAAGAAGGTGCTCAACAG | 625-652 | 15 | |
| Bgp127SD | B. bissettii | GAAGGTGTTCAGCAAGAAGG | 637-656 | 15 | |
| ospA | N1 | B. burgdorferi sensu lato | GAGCTTAAAGGAACTTCTGATAA | 184-206 | 14 |
| C1 | B. burgdorferi sensu lato | GTATTGTTGTACTGTAATTGT | 745-722 | 14 | |
| Detect. probe | B. burgdorferi sensu lato | CTTGAAGGCGTAAAAGCTGACAAA | 226-249 | 12 | |
| SSO probe | B. burgdorferi sensu lato | ACTAATGTTTTGCCATCTTCTTTGAA | 329-304 | 28 | |
| p66 | outer1 | B. burgdorferi sensu lato | CGAAGATACTAAATCTGT | 147-158 | 8 |
| outer2 | B. burgdorferi sensu lato | GCTGCTTTTGAGATGTGTCC | 442-461 | 8 |