Table 3.
Variable Number of Tandem Repeat (VNTR) Loci Developed or Tested in This Study
| Locus namea | Consensus pattern | Primer IDb | Tm | Primer sequence | Size (bp)c |
|---|---|---|---|---|---|
| VPTR1 | ATGGTCATGGCCGTCATCATC | VPTR1-L (NED) | 60.1 | GAAAGCGATATTGCACGGTA | 179 |
| VPTR1-R | 59.7 | TCATGTTGAACACTCGCTTG | |||
| VPTR7 | ATAATTAAAACCG | VPTR7-L (VIC) | 59.7 | AAATTGAGTTCCTGCAACGA | 114 |
| VPTR7-R | 59.8 | GTGCGTGAAAGGTAGCAGTC | |||
| VPTR8 | AGGTTCT | VPTR8-L (PET) | 59.6 | CCAGATATGTCAGACAGTGACG | 152 |
| VPTR8-R | 61.3 | GACGCTTTCACGCCAACT | |||
| VPTR9 | ACAAGGTCAGACTCCC | VPTR9-L (6FAM) | 60.1 | TTTCCTTGTCTGGGAGACG | 134 |
| VPTR9-R | 58.6 | TTTATCCCTCATTCCACCAC | |||
| VPTR10 | TCAACTTC | VPTR10-L (VIC) | 60.4 | GGAAGACGATGTTGGTTGC | 145 |
| VPTR10-R | 59.7 | GGATTACTCAGCCGAGACG | |||
| VPTR11 | ACAAAGCAC | VPTR11-L (6FAM) | 60.1 | TTACTGAATGGAAGGCGTTG | 151 |
| VPTR11-R | 61.0 | TATCGCGAAGCAATCTCTCA | |||
| VPTR12 | TAGCTTGATAACTA | VPTR12-L (PET) | 59.9 | CGAATCGAAGACATGGGATT | 160 |
| VPTR12-R | 59.9 | TTACCAACGGCCAAGTAACC | |||
| LMTR1 | AGTACCRCCAACACC | LMTR1+ (PET) | 56.0 | AAAAGCCCCGATTGGATATG | 220 |
| LMTR1- | 56.0 | TTTTGTTGGTGGCACAGTTG | |||
| LMTR2 | ACACCAAAAGAT | LMTR2+ (NED) | 60.4 | AGTAAAAGGCATGGACTTAACGAA | 100 |
| LMTR2- | 58.8 | CTTCGTTTTACTTGGTTTTATTGGTAG | |||
| LMTR3 | TAAAACCTA | LMTR3+ (6FAM) | 61.1 | CACGTATGATCCAAATGAAGGAA | 274 |
| LMTR3- | 60.7 | TTTTGGTAATGGTTTTGCTTCTTC | |||
| LMTR8 | AACACCARKKCCARKSCCAAKWCC | LMTR8+ (6FAM) | 60.2 | TACAAGTGATTTTGCGACTGTTG | 248 |
| LMTR8- | 62.5 | TTTTGTGACTTGGCACTTCTGG | |||
| STTR3 | ACCCCGCCCGACGATAGCGGCGATGACGATGTG | STTR3-F (PET) | 57.0 | CCCCCTAAGCCCGATAATGG | 400 |
| STTR3-R | 59.6 | TGACGCCGTTGCTGAAGGTAATAA | |||
| STTR5 | CACGAC | STTR5-F (PET) | 61.7 | ATGGCGAGGCGAGCAGCAGT | 578 |
| STTR5-R | 56.9 | GGTCAGGCCGAATAGCAGGAT | |||
| STTR6 | GCAAGG | STTR6-F (6FAM) | 54.0 | TCGGGCATGCGTTGAAA | 578 |
| STTR6-R | 54.0 | CTGGTGGGGAGAATGACTGG | |||
| STTR9 | TGCGATGTC | STTR9-F (6FAM) | 60.6 | AGAGGCGCTGCGATTGACGATA | 536 |
| STTR9-R | 60.6 | CATTTTCCACAGCGGCAGTTTTTC | |||
| STTR 10pl-F (VIC) | 65.1 | CGGGCGCGGCTGGAGTATTTG | 370 | ||
| STTR10p | CCTGTT | STTR10pl-R | 66.6 | GAAGGGGCCGGGCAGAGACAGC |
a
VP, Vibrio parahaemolyticus; LM, Listeria monocytogenes; ST, Salmonella enterica serovar Typhimurium (Lindstedt et al., 2003, 2004).
b
NED, VIC, PET, and 6FAM indicate primers with 5-prime conjugated fluorophores when products were scored using an ABI 3730 Genetic Analyzer (Applied Biosystems, Foster City, CA).
c
Approximate size in base pairs; this will be variable between strains.