Table A2.
Intergenic primer pairs selected for real time RT-PCR.
| Primer paira | Strainb | Forward primer (5′-3′) | Reverse primer (5′-3′) |
|---|---|---|---|
| Cag1/2 | A | CGTTACCAACGAACCAACTGA | TCATTGAGCCATTTATTTCTCGTAA |
| Cag2/3 | A | GTGTAAATGGACTGCTAGTGTGGA | AGCGATACAGCGGTTGCTA |
| Cag2/3 | B | ATGTCCCAAATGCAACAGATTAA | CGGCTTCACTTATTTCTTTAGCATAA |
| Cag2/3 | C | TTCACTCCCAATGAGTTTTTTACA | CGGCTTCACTTATTTCTTTAGCATA |
| Cag3/4 | A | GTGTGGTTATGAGAGCGTTCAA | ATTTTTCTCGCCTGTTGTTCAA |
| Cag3/4 | B | AACTGCTTTCACCACTAAGGGA | GGATTTTTCTCGCTTGTTGTTCA |
| Cag3/4 | C | TGTGTGGTTATGAGAGCGTTCA | GGTGAGATTTTCGTATTGCTTGA |
| Cag4/5 | A | TTCTCAAGTGCGATATAACGAGTAGA | TCTTTAGTGCCTGTGGGTTCAA |
| Cag4/5 | B | CTAAGAGCGATGGTTGGCAA | AAAATATGATCTTTGTCTTGCATGAA |
| Cag4/5 | C | GGGGAATGAAACACAACCCTAA | GAAGGCAAAAAGCCTATTCCAA |
| Cag5/virB1 1 | U | ACCCTTTCTTTCAGCCCATCTATAA | TGTCCATATCAACCACCACAA |
| virB11/Cag 6 | U | AGGATTTAATGCCGCTTCTTTTAA | CAATGAGATGGTCCAAGATATAGGGA |
| Cag6/7 | U | GTTCCATTGCTGTTTCCTTTCA | AATCACCACAAGCCCCAAA |
| Cag7/8 | A, B | GGTGAATCTTGTTGGGCTTTTTTA | AGGATTGAGATGGTATAGAGTTAATGAAA |
| Cag7/8 | C | TTCAAGTTTATCGTTTTCTTCATTCA | ATGGTATAGAGTTAATGAAATTGCAGAA |
| Cag8/9 | U | AATAACCAAGACAGAAACAGCCAA | GATGGTAGCAGAATGGATAGAGAAA |
| Cag9/10 | U | AATAGCTTTCAACCAATTAGGAACAA | AACTCTTCTCAAGAAAATCTTATCATCAA |
| Cag10/11 | U | CCCAACCAAATTTTCATCAATCA | GTTTGAAGCAATCCGCTACTTACA |
| Cag11/12 | A, B | AAACAAGGCGGTGCAGAA | GGTGTGTCTTTGAGTTTGTCATTTAA |
| Cag11/12 | C | GCTTCATAGGTATGGGCTATTTGA | TGTTTCACCACTTTTTTCGCATA |
| Cag12/13 | U | AAATCAGAAGTTTGCTCAGTGGTAA | CGCTAATCTAAAAACCATTGAACAA |
| Cag13/14 | U | AGCGGTCATAATTCAAAGAGCAA | CAACAAGGCAATAGATTACTAGCT GAA |
| Cag14/15 | U | ACCAATCGCAAACAAATCAAA | GATATGGTGGTGGTTTTCCAA |
| Cag15/16 | A, C | AATACCAACAAGCCGCATACAA | CTCCAAACGCAACCAATGA |
| Cag15/16 | B | AATACCAACAAGCCGCATACAA | TGGATCAGATTAGGGATTATTGGAA |
| Cag16/17 | U | CGATCCTATGATGAGCGACAA | GATAGCGTTTAAGCCCCCATAA |
| Cag17/18 | U | GCTCTAAATCTGAACTGCCCAATA | GAACAAAGTAAGCGACAATACCTACA |
| Cag18/19 | U | GGCTAGTGGTTGAAAAAATCTCATCTA | AAAGAGAAACGACAGCAAGAAACA |
| Cag19/20 | U | ATAACGCCATTAGCCCCTTTTAA | GGGTGCAAACTAAAATAATCGTGAA |
| Cag20/21 | A, B | GATTAGTAAATCCCACAACAATAGGAATAA | TTTTTACCACCGATCTTAGGGTATTAA |
| Cag20/21 | C | GCGGTCATTTGCGGATTAGTA | GGCGATTACGGTCCAAACA |
| Cag21/22 | U | AGCGTTAAACATGCCAATGATAA | GATATGAGCGTTGAAGCTAAAAAGAA |
| Cag22/23 | U | TCACCTTCCATTTCTTCTTCTATGAA | GTTTTAATTTGAGGGGCATTCCTA |
| Cag23/24 | U | CGCTTTTGAACCTCTTGCTCTA | TCAGCACGACCAACAAACAA |
| Cag24/25 | U | CATACGAACTGAAAACAACGAGACTTA | ATATTGGCGAGAGTGGAGGA |
aOne primer was in the intergenic space and the other was sometimes located in an adjacent gene. bStrain specificity: A-26695, B-J99, C-J166, U-universal.