TABLE 2.

Primers used in this study

PrimerSequencePurposeReference
oriT-F5′-CAAATAAAATGACAGTCATC-3′oriT cloningThis study
oriT-R5′-GGCATCGCCCCATCAATT-3′oriT cloningThis study
int-101F5′-TGGCTCCCGCCACTGGTATC-3′int mutant constructionThis study
int-490R5′-CGGGACGCAACTTCCAGCAG-3′int mutant constructionThis study
virB1-60F5′-GTCCACGGCATTCGACGT-3′virB1 mutant constructionThis study
virB1-359R5′-CGGTAGCAGTCTCTGAG-3′virB1 mutant constructionThis study
mobB-101F5′-TGCAACAGAAACAACTGGTG-3′mobB mutant constructionThis study
mobB-500R5′-TAATGCAGTGTTTGCGGCAG-3′mobB mutant constructionThis study
15′-GCACACAGGCATTTTCCAGCAG-3′Detection of excisionThis study
25′-AGATGGCTGGATAGGCAC-3′Detection of excisionThis study
35′-GACCCAGATACAGATAGC-3′Detection of excisionThis study
45′-GGCTGACGTTGCCGACGATAAG-3′Detection of excisionThis study
1′5′-GGTGACGTTCAAGAGAGACC-3′Detection of excisionThis study
2′5′-AGAAGGCTTGAGGGTGCGGATT-3′Detection of excisionThis study
3′5′-GACTCATACCGCTCATGGGCAC-3′Detection of excisionThis study
4′5′-GTGAATTCATCCTACTGGC-3′Detection of excisionThis study
1166F5′-GGTGCTCTTTACATCATTGC-3′magA detection29
500R5′-GTTCACAACAGCTGCCTGAC-3′magA detection29
7C4-T715′-ATCCTGGAAGCTCACCGTTC-3′kfu/PTS region detection29
26D6-T325′-ATTTCCACGCGGATACCGTC-3′kfu/PTS region detection29
10E4-2-5F5′-AGTCGGCCTGGGGTTTAAGG-3′allS region detection29
10E4-2-475R5′-CAGTCAACGTGGCGATTCGC-3′allS region detection29
asn1-F5′-GTAGACGTGAGAATGGCCTG-3′ICE integration site analysisThis study
asn1-R5′-GACAGGCTGTTTTCAGCATC-3′ICE integration site analysisThis study
asn2-F5′-CTGGGAGTATGATGCACTGG-3′ICE integration site analysisThis study
asn2-R5′-GGTTAATGATCGGCCATTGC-3′ICE integration site analysisThis study
asn4-F5′-GTCGCTGTCGTGGACTTTAC-3′ICE integration site analysisThis study
asn4-R5′-AGTGATCCTGATGTCGCTGG-3′ICE integration site analysisThis study
asn3-F5′-AAGATACGACTCCACACG-3′ICE integration site analysisThis study
ybtS-R inverse5′-CGCCCTATTTAATGGTGTAG-3′ICE integration site analysisThis study
fyuA-F5′-ATGAAAATGACACGGCT-3′5′ region prevalence analysisThis study
fyuA-R5′-TCAGAAGAAATCAATTC-3′5′ region prevalence analysisThis study
virB1-F5′-ATGCTTTCCACCACAGC-3′3′ region prevalence analysisThis study
virB1-R5′-TTATTCCTCCTCCTCAC-3′3′ region prevalence analysisThis study
iroN-F5′-GTCCGGCGGTAACTTCAGCC-3′Middle region prevalence analysisThis study
iroN-R5′-TCAGAATGATGCGGTGACAC-3′Middle region prevalence analysisThis study
HPI 3′-F5′-CTGCGGTAAATAAATGACG-3′Connection of 5′ and 3′ regionsThis study
virB1-F inverse5′-GCTGTGGTGGAAAGCAT-3′Connection of 5′ and 3′ regionsThis study
orf3-R5′-CTTGATGAAAATCTGGTG-3′Left junction of middle regionThis study
orf16-F5′-AATGTTCTCTGCGCATGG-3′Right junction of middle regionThis study
asn probe-F5′-CGTTCACACGATTCCTC-3′asn tRNA probeThis study
asn probe-R5′-GGCTTCTTAAATTTGGCTC-3′asn tRNA probeThis study