Table 3.
Primers used for amplification and sequencing of MUCVa.
| Primer nameb | Genomic position (No. of nucleotides) |
Sequence (5’ → 3’) | Estimated melting temperature (°C) |
|---|---|---|---|
| MUCV 26S (+)c | 7429 – 7445 (17) | TAGTYCAGTCCGCAACC | 57.1 |
| MUCV 6kE1(−)c | 9876 – 9890 (15) | GTGTTCGTAGGCGCC | 58.7 |
| MUCV 5’E2 (+)c | 8561 – 8575 (15) | CGACGGGCAYGACGG | 66.7 |
| MUCV 3’E1 (−)c | 11183 – 11209 (23) | TAATTATGTTTCTGGTTGGTCAG | 59.4 |
| MUCV 7637 (−) | 7637 – 7654 (18) | TTAGCAGGTGGCCCCTCG | 68.5 |
| MUCV 7611 (+) | 7611 – 7626 (16) | TCCAATGCAACCAGCG | 62.4 |
| MUCV 7930 (+) | 7930 – 7947 (18) | TTGCCTCCCTGAAGACGA | 64.7 |
| MUCV 8138 (−) | 8138 – 8155 (18) | TCTAGTATGGGGCGTCCA | 61.7 |
| MUCV 8432 (+) | 8432 – 8449 (18) | CCGGCAGACAGAAGAGAT | 60.5 |
| MUCV 8638 (−) | 8638 – 8655 (18) | CTCTGCTCTTAACGTTCC | 54.9 |
| MUCV 8639 (−) | 8639 – 8659 (21) | ACTCTGCTCTTAACATTCCCG | 68.9 |
| MUCV 8811 (+) | 8811 – 8828 (18) | TCCTGTTCAGTGCCTTAT | 55.5 |
| MUCV 8942 (+) | 8942 – 8959(18) | AAGATGCGTATGTGGAGA | 56.5 |
| MUCV 9128 (−) | 9128 – 9145(18) | TACGCGCGGCATTGTGAT | 68.7 |
| MUCV 9132 (−) | 9132 – 9149 (18) | TACGCGCGGCATTGTGAT | 68.7 |
| MUCV 9311 (+) | 9311 – 9328 (18) | ACGGAATCCGACATATTT | 56.7 |
| MUCV 9430 (+) | 9430 – 9447 (18) | GTTTGGGGTAATCACCCG | 62.6 |
| MUCV 9638 (−) | 9638 – 9655 (18) | GGAGTCAAACAAGATACT | 48.0 |
| MUCV 9641 (−) | 9641 – 9658 (18) | CGGAGTCAAACAAGATAC | 52.6 |
| MUCV 9812 (+) | 9812 – 9829 (18) | CCGCTTGCTGAAGTGCAT | 65.3 |
| MUCV 10137 (−) | 10137 – 10154 (18) | GATACACCCCCGTGAAGA | 60.9 |
| MUCV 10311 (+) | 10311 – 10328 (18) | GCGGTAGTGTACGTGAAT | 55.9 |
| MUCV 10624 (−) | 10624 – 10641 (18) | TGTACTTTAATGATGGTG | 48.2 |
| MUCV 10822 (+) | 10822 – 10839 (18) | GGATCGCCACTGTCAAGT | 61.4 |
a
MUCV = Mucambo virus (VEEV subtype IIIA virus).
b
(+), positive sense primer; (−), negative sense primer.
c
Amplification and sequencing primers.