Table 1.
New primers used in this study.
| Target Locus | Primer Name | Nucleotide Sequence | PCR Program | Size (bp)1 |
|---|---|---|---|---|
| New 3-primer combinations | ||||
| RD8 | RD8flnkF | 5' CAT GCT AAG CAG ATC GTC AGT TTT GA 3' | 1a, 1b | 289/485 |
| RD8iF | 5' GCC GCA TTG TCG GGG TGC GAT TCC CAC ACC 3' | |||
| RD8flnkR | 5' CGG TTC CGG CGG GCT CCG GAT TGC TGT ACT 3' | |||
| RD9 | RD9flnkF | 5' ACT CCC AGC GCT CGG CGG TGA CGG TAT CGT 3' | 1a, 1b | 293/499 |
| RD9iR | 5' ATT CCG TGG GCG CTG CGG CCA ATG TTT GTT 3' | |||
| RD9flnkR | 5' GTG GCT CGG CAC GCA CAA CTC GTT CAA CAG 3' | |||
| RD10 | RD10flnkF | 5' GCG CCA CCT CGG CCG GAT TCC TGC AAC CAT 3' | 1a, 1b | 291/478 |
| RD10iR | 5' TTC GGC CTT GCC GTC ATA GCG CAA TAG CGA 3' | |||
| RD10flnkR | 5' CTC GGC GGC AAG TCG GCG GCC ATC ATT CTC 3' | |||
| RD701 | RD701flnkF | 5' ACT CGC CGG CTG TGC AGG TGG TCG TT 3' | 1a, 1b | 350/487 |
| RD701iR | 5' CCA AAA TTG TCG CCC TTC AGT GCG GTA TCC 3' | |||
| RD701flnkR | 5' GAG GGG CAG CGC GGG GAA GTC G 3' | |||
| TbD1 | TbD1flnkF | 5' CTA CCT CAT CTT CCG GTC CA 3' | 1a, 1b | 298/485 |
| TbD1iF | 5' AAG GAA CTG CGA GAT AGG ATC GCC AAT TTC 3' | |||
| TbD1flnkR | 5' CAT AGA TCC CGG ACA TGG TG 3' | |||
| New primers for PCR-RFA | ||||
| Rv1332523 | Rv1332F | 5' GCC CTG CGC AGC CTG CAC GAA CCT GAG ATT 3' | 1a, 1b | 344 |
| Rv1332R | 5' GGA TGC CCC CGA CGT CGG TGA TGG AGT TCA 3' | |||
| nat751 | nat751F | 5' ACC CGG CAT CGA AGT TCG TCA CGG GAC TGA 3' | 2a, 2b | 766 |
| nat751R | 5' TGG TGT ACC AGG GGG CAC CGC AAA CCA G 3' | |||
| New amplification primers | ||||
| nat | natF | 5' ATC GGT GCG ACA TAG TTG G 3' | 2a, 2b | 1069 |
| natR | 5' GCC TTC TGC TCA AAG TTG CT 3' | |||
| Additional sequencing primers | ||||
| nat | natiF | 5' CAC CGA CCT CAC CGC TTC 3' | ||
| natiR | 5' GTC CTC GAG CCG ATA AGG TT 3' | |||
| Corrected primer from ref. 7 | ||||
| katG203 | katG203R | 5' CAA GAA GCT CTC ATG GGC GGA CCT GAT TGT 3' | ||
1 for RD loci, expected band sizes given as intact/deletion present