Table 1.
Primers and probes used.
| Primers/probes | Strains | Genome position | Sequences (5′–3′) |
|---|---|---|---|
| CP5 | Alfort/187 | 11874-11895 | GTAGCAAGACTGGRAAYAGGTA |
| CP6 | Alfort/187 | 12240-12219 | AAAGTGCTGTTAAAAATGAGTG |
| CP3F | Alfort/187 | 12106-12126 | ACCCTRTTGTARATAACACTA |
| CP3R | Alfort/187 | 12234-12209 | GTTAAAAATGAGTGTAGTGTGGTAAC |
| G1 | Alfort/187 | 12094-12118 | HEX-ACCCGCCAGTAGGACCCTATTGTAG-BBQ |
| G2 | 93-TD | 12084-12106 | Cy5-CTTGACCGGGCCCTATCAGTGGA-BBQ |
| G3 | P97 | 12063-12086 | FAM-CACGTGAGTGCGGGTAGCCCAA-BBQ |
Y: C or T. R: A or G. HEX: 5′-hexachloro-fluorescein-CE phosphoramidite. BBQ: 4,4-bis-(2-butyloctyloxy)-p-quaterphenyl. Cy5: cyanine 5. FAM: 6-carboxy-flourescein.