TABLE 2.

Sequence of oligonucleotide probes and primers used to analyze the RS1Φ genome

Primer	Sequence of probe or primer	Description and/or specificity	Source or reference
1	5′-TCTATCTCTGTAGCCCCTATTACG	Specific for the plus strand of ctxA gene and hence the single-stranded genome of CTXΦ	8
2	5′-CTCAGACGGGATTTGTTAGGCACG	Specific for minus strand of ctxA gene	8
3a	5′-ATGAGTTTGAAACCATACACTTT	Forward primer for rstC and specific for the minus strand of the RS1 element	This study
3b	5′-TTACAGTGATGGATCAGTCAAT	Reverse primer for rstC and specific for the plus strand of the RS1 element	This study
4a	5′-GCCTAAATCCGCAACTCAAGG	Forward primer for rstC and specific for the minus strand of the RS1 element	This study
4b	5′-CAATGGTACTGACGACTGCCCC	Reverse primer for ig1 and specific for the minus strand of the RS1 element	This study