TABLE 1.
Sequences of primers and TaqMan MGB probes
| SNP | 5′ to 3′ sequences for:
|
SNP change and genome position | GenBank accession no. | |
|---|---|---|---|---|
| Primers | TaqMan MGB probea | |||
| PS-1 | F-TGATGGTTTTGATTTCTTAGGCTTT | FAM-AAGGGTCACAACTC | G↔A, 7452 | NC_003980 |
| R-CACTTTGGTTGGATGGTTTAATGA | VIC-AAGGGTCGCAACTC | |||
| PS-52 | F-GTATCCTGAAATATAAAAGTGTAAAAGGTAAAAAATGGA | VIC-ATTAAGGACTCCCTCTTGGTT | A↔C, 72924 | NC_003981 |
| R-GATTCTTCAACGCAATATACCCTACTAAAATTATACTAT | FAM-AAGGACTCCCTATTGGTT | |||
| Branch1-7 | F-TCACCTCAATGACATCGCCA | FAM-CAAACCAATACCCCTTT | C↔A, 433277 | NC_003997 |
| R-TTGTTGTGAAGACGGATAACTTTTATG | VIC-CAAACCAATAACCCTTT | |||
| Branch1-26 | F-GACGGGAGCCAACCAGAA | FAM-ATAGCTTTTTTTCTATTCC | T↔C, 4624132 | NC_003997 |
| R-CCGTTGAATAAGCAGTATGAAATTTC | VIC-ATAGCTTTTTCTCTATTCC | |||
| Branch1-28 | F-AATATCTTTCATACAAGGCGCACTACT | FAM-CGTTGTAGTTATTTTAC | T↔G, 4929186 | NC_003997 |
| R-CCATAATCGTGCTTGTCCAAATC | VIC-CGTTGTAGGTATTTTAC | |||
| Branch1-31 | F-GAAGAACAAGCGAAAGACGTACCT | VIC-CGGTTCACATGGCAT | A↔G, 2749543 | NC_003997 |
| R-GTAGTTCATAACGTTTGAAAAAGTAGGGATA | FAM-TCGGTTCACATAGCAT | |||
a
Note that all probes have a minor-groove binder, nonfluorescent quencher attached to the 3′ end. FAM, 6-carboxyfluorescein. The Ames probes were labeled with FAM except in the case of PS-1, which was labeled with VIC. Underlined letters indicate SNP location.
b
SNP changes are expressed as “Ames ↔ non-Ames.”