TABLE 2.
Primer sequences and characteristicsa
| Primer name | Sequence (5′→3′) | Tm (°C) | Amplicon size (bp) | Position in RM1221 genome |
|---|---|---|---|---|
| Cje0215F | GCG AGT GAA GGC AAA AG | 46.0 | 351 | 207652-207668 |
| Cje0215R | TTC TCC ATA GCA AGT GAT AAA C | 46.0 | 208002-207981 | |
| Cje0251F | ATG GGG ATA AAT TTA GCA CTT G | 49.8 | 392 | 230266-230287 |
| Cje0251R | TAG GCC TTT AAC TTC ACT TTC AC | 49.5 | 230657-230636 | |
| Cje0270F | TTC ACC GCA AAG ATA AAA CTA A | 49.3 | 373 | 241603-241582 |
| Cje0270R | ACT ATA ATA TCA GCT GGG GAA CTA | 48.4 | 241231-241254 | |
| Cje0544F | AAT AGG GGA ATG CCA AAA A | 49.0 | 357 | 498853-498871 |
| Cje0544R | CTA CTA ATC TCA AAT ATC CTA CAT | 41.6 | 499209-499186 | |
| RMCj212F | CGA ATT TCG AGC TTT ACA GT | 54.9 | 206651-206670 | |
| RMCj275R | AAA ATG CGA ACA AGT TCA TT | 55.0 | 244602-244583 | |
| Cje0213F2 | TGA CTT TAA GGT TTG GAG GAT A | 55.7 | NA | |
| Cje0343F2 | ACT TTT TCT CAT TTT TGC ATA CC | 55.3 | NA | |
| Cje0344F | GCG ATC TAA TTC TTT ACC CAT A | 55.3 | NA | |
| Cje0344R | TTG ATA CCA ATT CTT CTT GTC A | 55.0 | 309513-309492 | |
| 344jk1 | TGA AAG TGA CTT CAA AGA AAA G | 54.1 | NA | |
| 522jk1 | TTA TTG CTT CTG CAT ATT CAT C | 54.8 | NA | |
| 522jk2 | ACG GCT TTA GTA TTA GCT TTT G | 55.0 | NA |
a
Primers were used to generate PCR amplicon probes for Southern hybridizations, to sequence the lambda library, or to investigate bacteriophage insertion sites. Primers were based on the bacteriophage genes present in RM1221 (GenBank accession number CP000025) or on the sequence obtained from isolate 00-2425. Tm, melting temperature of the primer; NA, not applicable (the sequence is not present in RM1221).