Table 3.
Primers used in this study for MLVA and SNR analyses
| LOCUS | PRIMER SEQUENCE (5' to 3') | CONCENTRATION μM | |
|---|---|---|---|
| MLVA 25 | |||
| CG3 | F:CY5.5-TGTCGTTTTACTTCTCTCTCCAATAC R:AGTCATTGTTCTGTATAAAGGGCAT |
0.30 | |
| bams44 | F: CY5.5-GCACTTGAATATTTGGCGGTAT R: GCGAATTAATTGCTCCTCAAAT |
0.30 | |
| bams3 | F: CY5.5-GCAGCAACAGAAAACTTCTCTCCAATAACA R:TCCTCCCTGAGAACTGCTATCACCTTTAAC |
0.30 | |
| Multiplex A | vrrB2 | F: D2-CACAGGCTATTCTTTATCAAACTCATC R: CCCAAGGTGAAGATTGTTGTTGA |
0.15 |
| bams5 | F: D2-GCAGGAAGAACAAAAGAAACTAGAAGAGCA R: ATTATTAGCAGGGGCCTCTCCTGCATTACC |
0.30 | |
| bams15 | F: D2-GTATTTCCCCCAGATACAGTAATCC R: GTGTACATGTTGATTCATGCTGTTT |
0.60 | |
| bams1 | F: CY5-GTTGAGCATGAGAGGTACCTTGTCCTTTTT R: AGTTCAAGCGCCAGAAGGTTATGAGTTATC |
0.15 | |
| vrrC1 | F: CY5-GAAGCAAGAAAGTGATGTAGTGGAC R: CATTTCCTCAAGTGCTACAGGTTC |
0.30 | |
| bams13 | F: CY5.5-AATTGAGAAATTGCTGTACCAAACT R: CTAGTGCATTTGACCCTAATCTTGT |
0.30 | |
| vrrB1 | F: CY5--ATAGGTGGTTTTCCGCAAGTT R: GATGAGTTTGATAAAGAATAGCCTGTG |
0.10 | |
| Multiplex B | bams28 | F: CY5-CTCTGTTGTAACAAAATTTCCGTCT R: TATTAAACCAGGCGTTACTTACAGC |
0.15 |
| vrrC2 | F: CY5-CCAGAAGAAGTGGAACCTGTAGCAC R: GTCTTTCCATTAATCGCGCTCTATC |
0.10 | |
| bams53 | F: D2-GAGGTGTGTTAGGTGGGCTTAC R: CATATTTTCACCTTAATTTTGGAAG |
0.60 | |
| bams31 | F: D2-GCTGTATTTATCGAGCTTCAAAATCT R: GGAGTACTGTTTGTTGAATGTTGTTT |
0.60 | |
| vrrA | F: CY5.5-CACAACTACCACCGATGGCACA R: GCGCGTTTCGTTTGATTCATAC |
0.06 | |
| bams25 | F: CY5.5-CCGAATACGTAAGAAATAAATCCAC R: TGAAAGATCTTGAAAAACAAGCATT |
0.15 | |
| Multiplex C | bams21 | F: CY5.5-TGTAGTGCCAGATTTGTCTTCTGTA R: CAAATTTTGAGATGGGAGTTTTACT |
0.30 |
| bams34 | F: D2-TGTGCTAAATCATCTTGCTTGG R: CAGCAAAATCAATCGAATCAAA |
0.30 | |
| bams24 | F: CY5-CTTCTACTTCCGTACTTGAAATTGG R: CGTCACGTACCATTTAATGTTGTTA |
0.30 | |
| bams51 | F: CY5-ATTTCCTGAAGCAGGTTGTGTT R: TGCATCTAACAATGCAGAACAA |
0.60 | |
| bams22 | F: CY5-ATCAAAAATTCTTGGCAGACTGA R: ACCGTTAATTCACGTTTAGCAGA |
0.15 | |
| Multiplex D | bams23 | F: D2-CGGTCTGTCTCTATTATTCAGTGGT R: CCTGTTGCTCCTAGTGATTTCTTAC |
0.30 |
| bams30 | F: CY5.5-AGCTAATCACCTACAACACCTGGTA R: CAGAAAATATTGGACCTACCTTCC |
0.30 | |
| pXO1 | F: CY5-CAATTTATTAACGATCAGATTAAGTTCA R: TCTAGAATTAGTTGCTTCATAATGGC |
0.15 | |
| pXO2 | F: CY5.5-TCATCCTCTTTTAAGTCTTGGGT R: GTGTGATGAACTCCGACGACA |
0.15 | |
| STR-MTD | |||
| Singleplex A | CL33 | F: 6FAM-TGGGGTATATTCCCATCGAA R:CCGCAGATACCAACCAACAT |
0.2 |
| Singleplex B | CL12 | F: 6FAM-AAGCCAGGTGCAAAAACAGT R: TCTCACTGTGCCTCGCTAAA |
0.2 |
| Singleplex C | CL1 | F: 6FAM-TTCTCGGAGATGATTTTCGG R:CTCCCATTTTACATCCCCCT |
0.2 |
| Singleplex D | CL37 | F: NED-CTCCGCAATTTTCAAACGAT R: CCGCCGGCATAAAGATAGTA |
0.2 |
| KEN-MTD | |||
|
CL33 HM1 |
F: PET GAAAACTTTGCAACCGACC R: GTCGAACGTGTTCTAGCTACAG |
0.2 | |
| Multiplex I |
CL10 HM6 |
F: 6FAM-TAAAAAGACAGAATTTTCAATTTTATCAACAAC R: GTGGAAACTAATGTGAGTTATATATGTTAGTTAAG |
0.2 |
|
CL12 HM2 |
F: VIC-GCTATTCTCACTGTGCCTCG R: GTTAAAACGAAGTAAAGAAAAGTGGG |
0.2 | |
|
CL35 HM13 |
F: NED-GGATTGCTTAAGGTATATAATGGATTT R: GTTGTGTTCCATATGTATCCCTCC |
0.1 | |