TABLE 2.
Primers and probes used in this study
| Primer or probe | Sequence (5′-3′) |
|---|---|
| Primers | |
| c14Bam | CCGGGGATCCGATTACACAGGCTAAGGAGG |
| c14Eco | CACGGAATTCCGATTATTTTTCCCGGATGG |
| deeplac | CGGGCCTCTTCGCTA |
| EcopBAD2 | CGACGAATTCTCCCGCCATTCAGAGAAGAAACC |
| luxS(T-7A) For | CGGAGGAGGCTAAATGCCGTTGTTAGATAG |
| luxS(T-7A) Rev | CTATCTAACAACGGCATTTAGCC |
| luxSKO For | GAAAGAGTTCAGAAAATTTTTAAAAAAATTACCGGAGGTGGCTAAGTGTAGGCTGGAGCTGCTTC |
| luxSKO Rev | TGAACTGGCTTTTTTCAATTAATTGTGAAGATAGTTTACTGACTACATATGAATATCCTCCTTAG |
| lsrACDBFGKO For | AATACATTTGTTCAAAACTCACCTGCAAAACTGAACGGGGGAAATGTGTAGGCTGGAGCTGCTTC |
| lsrACDBFGKO Rev | CGTCAGCGCGTTACCCCAATTGTAGATAAAATTGATAAATTCGCCCATATGAATATCCTCCTTAG |
| M13For(−20) | GTAAAACGACGGCCAG |
| nadE(T-3A C-2T A-1G)-lacZ For | CTTTTTATCGCAACTCTCTACTGTTTCTCCATCTTTTCTGTCTGGAGGGGTATGATGACATTGCAACAAGTCG |
| ompXSma | CGACTCCCGGGCAGTGCTGAAAGACATGCAATTTTTTTCATAACCACCTC |
| pBAD-DNA-RACE | ACCTGACGCTTTTTATCGCAACTCTCTACTGTTTCTCCAT |
| pBAD-luxS4-lacZ | AACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGGTATGATCGACTGTGAAGCTATC |
| pBAD-nadE-lacZ For | ACCTGACGCTTTTTATCGCAACTCTCTACTGTTTCTCCATCTTTTCTGTCTGGAGGGGTTC |
| pBAD-nadE-lacZ Rev | AACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACTTGTTGCAATGTCATTGAACCC |
| pBADompX | CCAGATTATTCCTAATCACCAGACTAATGATTCCATCAATCCTGGATGGAGAAACAGTAGAGAGTTGCG |
| pBAD-yqaE-lacZ For | ACCTGACGCTTTTTATCGCAACTCTCTACTGTTTCTCCATGCTTAAGAGATAAAATCTCTTTTTAAACAA |
| pBAD-yqaE-lacZ Rev | AACGCCAGGGTTTTCCCAGTCACGACGTTGTAAAACGACGATGACGATTCTCCAGAAACC |
| pBR-placRyeE For | GCGTGACGTCGCTGAAAAACATAACCCATAAAATGCTAG |
| pBR-placRyeE Rev | GAGAATTCCCTTTTATTTCATTGTATTACGCGTAAAAAATAAGC |
| pBAD-X-lacZ For | GCGGATCCTACCTGACGC |
| RACE_nadE1 | GTTGTTGCAATGTCATTGAAC |
| RACE_yqaE2 | CCAAGCAGTGTCAACAGAA |
| RACE _ryeE1 | GGAGGTGGTTCCTGGTACAG |
| RACE_universal | GATATGCGCGAATTCCTGTAGAACGAACACTAGAAGAAA |
| ryeEKO For | GGAAAATTCTTAGAAACCGATCACATACAGCTGCATTTATTAAGGGTGTAGGCTGGAGCTGCTTC |
| ryeEKO Rev | GAAATAAATCCTTTTATTTCATTGTATTACGCGTAAAAAATAAGCCATATGAATATCCTCCTTAG |
| ryeEA44T For | GCTAGCTGTACCAGGAACCTCCTCCTTAGCCTGTGTAATCTC |
| ryeEA44T Rev | GATATTACACAGGCTAAGGAGGAGGTTCCTGGTACAGCTAGC |
| ryeET47A For | CTAGCTGTACCAGGAACCACCACCTTAGCCTGTGTAATCTCC |
| ryeET47A Rev | GGAGATTACACAGGCTAAGGTGGTGGTTCCTGGTACAGCTAG |
| ryeET50A For | CTGTACCAGGAACCACCTCCATAGCCTGTGTAATCTCCC |
| ryeET50A Rev | GGGAGATTACACAGGCTATGGAGGTGGTTCCTGGTACAG |
| ryeEG38C-G39A-A40T For | CCCATAAAATGCTAGCTGTACCACATACCACCTCCTTAGCCTGTG |
| ryeEG38C-G39A-A40T Rev | CACAGGCTAAGGAGGTGGTATGTGGTACAGCTAGCATTTTATGGG |
| yqaE(T7A C9G)-lacZ rev | GTTTTCCCAGTCACGACGTTGTAAAACGACGATGACGATTCTCCACATACCCATATGTACTCCCTATAAG |
| Probes | |
| cfaprobe1 | CCACCAGCCATCCATATAACTTTCGCCTAACCCCA |
| yqaEprde1 | CCCAACGGAACCCTTTACCGAGCAGCACGCCGAGC |
| flu-probe | CCCTGCAGGAGTGCATCGCCTTCACGGATGGTCAGGGTATCG |
| luxSprobe1 | TCCCTCTTTCTGGCATCACTTCTTTGTTCGGCACG |
| mscLprobe1 | CCCAGAGGAGGCATGATGATATCGGCAACCAGTGA |
| nadEprobe1 | GGTTAATACGCGATCCGGTTGAATAAAGGCAATGG |
| ompXprobe1 | TACGGAAGTACCTGCGGTGAAAGCCAGAACTGCGG |
| ryeEprobe1 | TGGTTCCTGGTACAGCTAGCATTTTATGGGTTATG |
| uspGprobe1 | CGGACATGTTGTTTAATGCGGGAAGGATCGATGGT |