TABLE 5 .
Primers used in this study
| Primer | Sequence (5′–3′)a | Application |
|---|---|---|
| Leader404-f | CGGggtaccCATCTCAATTAAGCAGCTA | Amplification for 404-bp leader |
| Leader252-f | CGGggtaccCACCTAACTCACTATCAAT | Amplification for 252-bp leader |
| Leader158-f | CGGggtaccCGTATTAAATGTAGTATACT | Amplification for 158-bp leader |
| CRISPR-r | CCGgagctcCCATCCCCTAAAAATTAATCC | Amplification for a native CRISPR array |
| CRISPR-Cas-f1 | TAACTCACTATCAATCATTTCTCCAC | Amplification for CRISPR-Cas locus |
| CRISPR-Cas-r1 | GCATAATCCATCATCATTAATATCTATG | Amplification for CRISPR-Cas locus |
| CRISPR-Cas-f2 | TATAGAACTATTTGGCGTAATG | Amplification for CRISPR-Cas locus |
| CRISPR-Cas-r2 | GTAATCTTGCTTCTTCATAACT | Amplification for CRISPR-Cas locus |
| CRISPR-Cas-f3 | TTTATGGTTGGAGGTATAAGTATGAC | Amplification for CRISPR-Cas locus |
| CRISPR-Cas-r3 | TATATTATACTATATTTCCCCATGCC | Amplification for CRISPR-Cas locus |
| R1-S1-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-1, pLI-11, pLI-12 |
| S1-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCCTGATTCAGGTTACGGACAAGGTGAAATACTGATT | pLI-1,pLI-11, pLI-12 |
| R2-S2-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACCAATATGTATGCTTTGGTCTTTCTGCATTCCTGGA | pLI-12 |
| S2-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTCCAGGAATGCAGAAAGACCAAAGCATACATATTG | pLI-12 |
| R1-mecAC-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACGCAGTACCGGATTTGCCAATTAAGTTTGCATAA | pLI-C |
| mecAC-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTTATGCAAACTTAATTGGCAAATCCGGTACTGC | pLI-C |
| R1-mecAT-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACTTATGCAAACTTAATTGGCAAATCCGGTACTGC | pLI-T |
| mecAT-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCGCAGTACCGGATTTGCCAATTAAGTTTGCATAA | pLI-T |
| R1-S17-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACATTTCACCTTGTCCGTA | pLI-S17 |
| S17-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTACGGACAAGGTGAAAT | pLI-S17 |
| R1-S20-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACATTTCACCTTGTCCGTAACC | pLI-S20 |
| S20-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCGGTTACGGACAAGGTGAAAT | pLI-S20 |
| R1-S21-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACATTTCACCTTGTCCGTAACCT | pLI-S21 |
| S21-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCAGGTTACGGACAAGGTGAAAT | pLI-S21 |
| R1-S22-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACATTTCACCTTGTCCGTAACCTG | pLI-S22 |
| S22-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCCAGGTTACGGACAAGGTGAAAT | pLI-S22 |
| R1-S23-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACATTTCACCTTGTCCGTAACCTGA | pLI-S23 |
| S23-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTCAGGTTACGGACAAGGTGAAAT | pLI-S23 |
| R1-S25-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACATTTCACCTTGTCCGTAACCTGAAT | pLI-S25 |
| S25-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCATTCAGGTTACGGACAAGGTGAAAT | pLI-S25 |
| R1-S33-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACTAATCAGTATTTCACCTTGTCCGTAACCTGAAT | pLI-S33 |
| S33-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCATTCAGGTTACGGACAAGGTGAAATACTGATTA | pLI-S33 |
| R1-S36-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-S36 |
| S36-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCCTGATTCAGGTTACGGACAAGGTGAAATACTGATTA | pLI-S36 |
| R1-S39-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTA | pLI-S39 |
| S39-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTA | pLI-S39 |
| R1-S42-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATA | pLI-S42 |
| S42-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTATTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTA | pLI-S42 |
| R1-S45-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGAACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAGCTAATAATA | pLI-S45 |
| S45-R2-r | CACTCTGTCCCCTATTCTTCGGGGTAGTTATCGATCTATTATTAGCTGATTCAGGTTACGGACAAGGTGAAATACTGATTA | pLI-S45 |
| R1-S36m1-f | GATCGATAACTACCCCGAAGAATAGGGGACGACAACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M1 |
| R1-S36m2-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGGACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M2 |
| R1-S36m3-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGGGCTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M3 |
| R1-S36m4-f | GATCGATAACTACCCCGAAGAATAGGGGACGAGTTCTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M4 |
| R1-S36m5-f | GATCGATAACTACCCCGAAGAATAGGGGACGACGGTTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M5 |
| R1-S36m6-f | GATCGATAACTACCCCGAAGAATAGGGGACGTGGACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M6 |
| R1-S36m7-f | GATCGATAACTACCCCGAAGAATAGGGGTACAGAACTAATCAGTATTTCACCTTGTCCGTAACCTGAATCAG | pLI-M7 |
| mecA-f | TAATAGTTGTAGTTGTCGGGTTTGG | mecA detection |
| mecA-r | CATCGTTACGGATTGCTTCACTGTT | mecA detection |
| cas6-f | TTTAGGAAGTATTTTACATGGCGTG | cas6 detection |
| cas6-r | CCAGAAAATTCACCAAACTTCAATA | cas6 detection |
| CRISPR-RT-f | GGGACGAGAACTTCAAAT | qRT-PCR |
| CRISPR-RT-r | CAGTATGAAACAAATCAAGGT | qRT-PCR |
| mecA-r-biotin | ATTCAGGTTACGGACAAGGTGAAATACTGATTA | Northern blotting |
a
Nucleotides in the restriction sites are indicated by lowercase letters.