Table 3.
Primer sequences and specific PCR conditions for each marker region.
| Marker region | Amplicon size | Primer sequences: 5′–3′’ | Specific PCR cycling conditions |
||
|---|---|---|---|---|---|
| Annealing temp. (°C) | Extension duration (min) | No. PCR cycles | |||
| M1: C-C | 765 | F: AGATTTGTCCACGCCCACAT | 56 | 1 | 40 |
| R: TCAAATTGGGAGATGCCAGCT | |||||
| M2: LORF11 | 584 | F: GGGTTGCACAATCTTCTCAAA | 55 | 1 | 45 |
| R: ACGTCCGTTTCTCCAGAATG | |||||
| M3: meq | 1251 | F: GAGGTTGGTGCTGGAATGTT | 57 | 1.25 | 40 |
| R: AATGCCTTTAACCCTTTCCTTT | |||||
| M4: ICP4 (prox.) | 849 | F: AAACCCCATTTTCGTGCAGC | 56 | 1 | 40 |
| R: GCAAATGCGTTACCTGGAAA | |||||
| M5: ICP4 (dist.) | 482 | F: GAGGAGGATGTCACCCTGAA | 54 | 1 | 42 |
| R: CACAACCTCATCTCCACGAA | |||||
| M6: pp38 | 824 | F: CAGAATCCACTCCCCCAACGACA | 57 | 1 | 40 |
| R: CGAAGCAGAACACGAAGG | |||||
| M7: UL36 | 401 | F: ACCGCCACTACCGTTACATC | 55 | 1 | 40 |
| R: GCGCCTCGTCAAATATCC | |||||
| M8: UL43 | 340 | F: TGGTACTCGGGCCAACTTTA | 55 | 1 | 40 |
| R: CCGATGGTACCTTTGTTTTCA | |||||
Two additional primers, internal to those provided in Table 3, were also employed for sequencing M3 (meq): F2, 5′-AGAAGACGCAGGAAGCAGAC-3′); R2, 5′-GGTACACGGCTCGGTAACAG-3′.