TABLE 1.
PCR primers, primer and capture probe sequences, sizes of PCR amplicons, and references used in this studya
| Primer name | Sequence | PCR amplicon size | Reference(s) | Tm (°C) |
|---|---|---|---|---|
| UB-FW | 5′-Cy5-GCTAACTCCGTGCCAGCAGCCGCGG-3′ | 307 bp | Bang et al. (1) | 86.9 |
| UB-RW | 5′-Cy5-GGGCGTGGACTACCAGGGTATC-3′ | 65.8 | ||
| UC-FW | 5′-Cy5-GCGAAGAACCTACCYGGRCTTGATA-3′ | 314 bp | Linton et al. (17); this study | 77.3 |
| UC-RW | 5′-Cy5-TCGCGRTATTGCGTCTCATTGTATATG-3′ | 75.9 | ||
| CC-FW | 5′-Cy5-GTTAAGAGTCACAAGCAAGT-3′ | 194 bp | O'Sullivan et al. (24); Keramas et al. (14) | 53.7 |
| CC-RW | 5′-Cy5-CTAAAAATATCTAAACTAAGTCG-3′ | 51.7 | ||
| CJ-FW | 5′-Cy5-CAAATAAAATTAGAGGTAGAATGT-3′ | 160 bp | Winters et al. (33); Keramas et al. (14) | 58.1 |
| CJ-RW | 5′-Cy5-CCATAAGCACTAGCTAGCTG-3′ | 57.3 | ||
| HIP-FW | 5′-Cy5-GTACTGCAAAATTAGTGGCG-3′ | 149 bp | Slater et al., (27a); Keramas et al. (14) | 61.1 |
| HIP-RW | 5′-Cy5-GCAAAGGCAAAGCATCCATA-3′ | 55.3 | ||
| POS CTRL | 5′-Cy5-CTAAGATTTTCTGCATAGCATTAAT-3′ | 25 nt | Keramas et al. (14) | 61.5 |
| UB CAP 1 | NH2-C6-AGTGATTCCGAGTAACGCTTGCACC | 25 nt | Keramas et al. (14) | 75.2 |
| UB CAP 2 | NH2-C6-CGGAGGGTGCAAGCGTTACTCGGAATCACTGGGC | 34 nt | This study | 88.3 |
| UC CAP 1 | NH2-C6-ACGTATTTAGTTGCTAACAGTTNGGCTGAGCACTC | 35 nt | Keramas et al. (14) | 81.0 |
| UC CAP 2 | NH2-C6-AGGAAGGTGTGGACGACGTCAAGTCATCATGGCC | 34 nt | This study | 89.2 |
| CJ CAP | NH2-C6-GATGAGCAAGGAGAAGGAGCTATAGGTTTAGGCGT | 35 nt | Keramas et al. (14) | 82.7 |
| HIP CAP | NH2-C6-ACGCCTGTTTTTCCTATTTCCTCATAAACCTCATA | 35 nt | Keramas et al. (14) | 78.6 |
| CC CAP | NH2-C6-TTGAGTTTTATCCTTTAACAAGTCCTGTAAAATTG | 35 nt | Keramas et al. (14) | 75.5 |
| POS and NEG CTRL CAP | NH2-C6-ATTAATGCTATGCAGAAAATCTTA | 24 nt | Keramas et al. (14) | 61.5 |
a
Abbreviations: Tm, melting temperature; nt, nucleotides; CAP, capture; POS, positive; NEG, negative; CTRL, control.