Table 3. Primers and Probes used to detect WNA clade specific SNPs.
| Locus Name 1 (GenBank ID: AE017334) | Primers 5′→3′ 2 | Probes 5′→3′ 3 |
| wna2994131 | F-GCACGGTCTTTCTAAATTCATTGTT | VIC-AAAGAACATAGGAGTTTAC |
| R-TGCGATTGGAGTTGCAAATAAT | FAM-AAAGAACATACGAGTTTAC | |
| wna3631093 | F-CAGAACCTACAGAACCATCATTAAAGAA | VIC-ATTGCTTACACTTCAGA |
| R-GTAAACCCATTACCACCACACTATGT | FAM-ATTGCTTACACTTCGGAC | |
| wna3682247 | F-ACATGTTCACTTCACACATTTTCTCA | VIC-ACTCTTGAACAAACCA |
| R-GCAATTGCAACAAGTCATCCA | FAM-ACTCTTGAACAAGCCAA | |
| wna3732539 | F-CTAAAAGCTCCAAATGCAATAGCA | VIC-CTGTTCCTGATAACAA |
| R-TGGTGGATCAAATGCAGTTAACTT | FAM-CTGTTCCTGATAATAA | |
| wna3774186 | F-CTTTGGTTTTCCTTTGGTATAATCTCTT | VIC-ATGGCACCTTTACATCT |
| R-TGACGTTGAAGGATGGAATATTTTTA | FAM-CAGATGGCATCTTT | |
| wna4461234 | F-TTTTGATGGAGAGATTTTGCTTTCT | VIC-TACGTTCTACAAATGGTACGT |
| R-GCGAAATCGAGCAAGGATTC | FAM-TACGTTCTACAGATGGT | |
| wna4718500 | F-GCATCACCATTTAGATCATAAACCA | VIC-AGCCATGTGTATAGAA |
| R-TGTCGTCGTACAGAAAGAAACGTT | FAM-AGCCATGTGTATGGAA | |
| wna237471 | F-TCGATGGTGCGAGCTTTTATATT | VIC-AATGAGCTCGGCACCAT |
| R-TGGTCATTGGTGGTATTTGCA | FAM-AATGAGCTCTGCACCA | |
| wna1141774 | F-CGGCTTTTTTTCATTACGCATTA | VIC-CATTTACCGTATTGTTTTG |
| R-AAAGAAAACAGAACATGCATTGATG | FAM-ATTTACCGCATTGTTTTG | |
| wna3368524 | F-CACGCTTATCGCCATCGAT | VIC-TCTACTGGCATTTCA |
| R-TGACGGAAGTGTAACGGAAGGT | FAM-TCTACTGGAATTTC |
1
The locus name correlates to the position on the whole genome sequence of the Ancestral Ames strain (AE017334).
2
F refers to the Forward primer whereas R refers to the Reverse primer.
3
Allele states are designated in red. VIC is the fluor conjugated to the 5′ end of the probe for one allele whereas FAM is the fluor conjugated to the 5′end of the alternate allele.