CoronaVR
Designed primers for SARS-CoV-2 (2019-nCoV)
| Gene | Primer ID | Primer sequence | Start-Stop | Genomic-Start-Stop | Tm (C) |
|---|---|---|---|---|---|
| ORF10 | Frag1.F5.1 Frag1.R5.1 |
TATATAAACGTTTTCGCTTTTC ATTAAAGTTAACTACATCTACTTG |
7-28 108-85 |
29564-29585 29665-29642 |
52.56 51.85 |
| ORF10 | Frag1.F3.1 Frag1.R4.1 |
TTTTCCGTTTACGATATATAGTC TTAAAGTTAACTACATCTACTTG |
24-46 107-85 |
29581-29603 29664-29642 |
53.32 51.14 |
| ORF10 | Frag1.F1.1 Frag1.R1.1 |
AAACGTTTTCGCTTTTCCGTTTAC CATCTACTTGTGCTATGTAGTTAC |
12-35 94-71 |
29569-29592 29651-29628 |
60.9 56.45 |
| ORF7b | Frag1.F1.1 Frag1.R3.1 |
ATGATTGAACTTTCATTAATTGAC TTCATTATGATCTTGCAGTTC |
1-24 117-97 |
27756-27779 27872-27852 |
53.71 53.43 |
| ORF7b | Frag1.F5.1 Frag1.R4.1 |
TTCATTAATTGACTTCTATTTGTG CAAGTTTCATTATGATCTTGCAG |
12-35 122-100 |
27767-27790 27877-27855 |
53.15 55.93 |
| ORF7b | Frag1.F3.1 Frag1.R5.1 |
TGACTTCTATTTGTGCTTTTTAG GATCTTGCAGTTCAAGTGAG |
21-43 109-90 |
27658-27680 27864-27845 |
54.69 56.1 |
| ORF6 | Frag1.F3.1 Frag1.R3.1 |
TTTCATCTCGTTGACTTTCAGG CATTGGTTGCTCTTCATCTAATTG |
4-25 174-151 |
27205-27226 27375-27352 |
57.85 58.27 |
| ORF6 | Frag1.F2.1 Frag1.R2.1 |
TCTCGTTGACTTTCAGGTTAC ATTGGTTGCTCTTCATCTAATTGAG |
9-29 173-149 |
27210-27230 27374-27350 |
57.12 59.16 |
| ORF6 | Frag1.F1.1 Frag1.R1.1 |
GACTTTCAGGTTACTATAGCAG GAATATTTATTCTCAGTTAGTGAC |
16-37 149-126 |
27217-27238 27350-27327 |
55.49 52.73 |
| ORF6 | Frag1.F4.1 Frag1.R4.1 |
GTTGACTTTCAGGTTACTATAG TGAGAATATTTATTCTCAGTTAG |
13-34 152-130 |
27214-27235 27353-27331 |
53.38 50.76 |
| E | Frag1.F5.1 Frag1.R5.1 |
ATGTACTCATTCGTTTCGGAAGAG ATATTGCAGCAGTACGCACAC |
1-24 137-117 |
26245-26268 26381-26361 |
60.29 60.82 |
| E | Frag1.F3.1 Frag1.R3.1 |
TACTCATTCGTTTCGGAAGAGAC ACAATATTGCAGCAGTACGC |
4-26 140-121 |
26248-26270 26384-26365 |
59.67 58.04 |
| E | Frag1.F2.1 Frag1.R2.1 |
GTACGTTAATAGTTAATAGCG AAGAATTCAGATTTTTAACACG |
29-49 202-181 |
26273-26293 26446-26425 |
50.93 52.48 |
| ORF7a | Frag3.F3.1 Frag3.R3.1 |
GAAAATTATTCTTTTCTTGGCACTG AGTAAAGTTCTTGAACTTCCTCTTG |
3-27 292-268 |
27396-27420 27685-27661 |
57.45 58.68 |
| ORF7a | Frag1.F2.1 Frag1.R2.1 |
TGAAAATTATTCTTTTCTTGGCAC CAAAGTGTTATAAACACTATTGC |
2-25 338-316 |
27395-27418 27731-27709 |
56.25 53.67 |
| ORF7a | Frag1.F4.1 Frag1.R4.1 |
AATTATTCTTTTCTTGGCACTG TTCCTCTTGTCTGATGAACAG |
6-27 276-256 |
27399-27420 27669-27649 |
54.79 56.93 |
| ORF8 | Frag1.F2.1 Frag1.R2.1 |
TGTTTTCTTAGGAATCATCACAAC TGAAATCTAAAACAACACGAAC |
12-35 361-340 |
27905-27928 28254-28233 |
57.07 54.89 |
| ORF8 | Frag1.F4.1 Frag1.R4.1 |
TTTTCTTAGGAATCATCACAACTG CAAGACTACCCAATTTAGGTTC |
14-37 295-274 |
27907-27930 28188-28167 |
56.84 56.29 |
| ORF8 | Frag1.F1.1 Frag1.R1.1 |
CTTAGGAATCATCACAACTG TCTAAAAAGTCTTCATAGAACG |
18-37 329-308 |
27911-27930 28222-28201 |
53.03 52.83 |
| ORF8 | Frag1.F5.1 Frag1.R5.1 |
CTTAGGAATCATCACAACTGTAG TACAAGACTACCCAATTTAGGTTCC |
18-40 297-273 |
27911-27933 28190-28166 |
56.25 59.64 |
| M | Frag1.F1.1 Frag1.R1.1 |
TACCGTTGAAGAGCTTAAAAAGCTC AATCCTGTAGCGACTGTATGCAG |
24-48 603-581 |
26546-26570 27125-27103 |
61.2 62.04 |
| M | Frag1.F3.1 Frag1.R3.1 |
GCAGATTCCAACGGTACTATTACCG ATGCAGCAAAACCTGAGTCACC |
4-28 586-565 |
26526-26550 27108-27087 |
62.86 62.99 |
| M | Frag1.F4.1 Frag1.R4.1 |
GGCAGATTCCAACGGTACTATTACC AACCTGAGTCACCTGCTACACG |
3-27 577-556 |
26525-26549 27099-27078 |
62.73 63.52 |
| M | Frag1.F5.1 Frag1.R5.1 |
TGAAGAGCTTAAAAAGCTCC GGTCTGTGTTTAATTTATAGTTG |
30-49 628-606 |
26552-26571 27150-27128 |
54.86 53.1 |
| ORF3a | Frag1.F5.1 Frag1.R4.1 |
TGTTTATGAGAATCTTCACAATTGG CGTCGGTTCATCATAAATTGG |
8-32 804-784 |
25400-25424 26196-26176 |
57.26 56.73 |
| ORF3a | Frag1.F1.1 Frag1.R1.1 |
GAGAATCTTCACAATTGGAAC GTGTGAATTTGGACATGTTC |
15-35 743-724 |
25407-25427 26135-26116 |
54.51 54.77 |
| ORF3a | Frag1.F2.1 Frag1.R2.1 |
TTATGAGAATCTTCACAATTGGAAC TCCATTACTGGATTAACAACTC |
11-35 782-761 |
25403-25427 26174-26153 |
57.3 55.17 |
| ORF3a | Frag1.F3.1 Frag1.R3.1 |
TTATGAGAATCTTCACAATTG GTCGGTTCATCATAAATTGG |
11-31 803-784 |
25403-25423 26195-26176 |
50.96 53.76 |
| N | Frag1.F1.1 Frag1.R1.1 |
GACCCCAAAATCAGCGAAATGCAC GTTGAGTCAGCACTGCTCATGG |
14-37 1250-1229 |
28287-28310 29523-29502 |
65.23 63.28 |
| N | Frag1.F4.1 Frag1.R5.1 |
CTGATAATGGACCCCAAAATC ATCATCCAAATCTGCAGCAG |
5-25 1206-1187 |
28278-28298 29479-29460 |
56.26 57.91 |
| N | Frag1.F2.1 Frag1.R2.1 |
ACCCCAAAATCAGCGAAATGC CATCCAAATCTGCAGCAGGAAG |
15-35 1204-1183 |
28288-28308 29477-29456 |
61.39 61.84 |
| S | Frag1.F4.1 Frag1.R4.1 |
TTGTTTTATTGCCACTAGTCTC TCATCAAATTTGCAGCAGGATC |
14-35 3773-3752 |
21576-21597 25335-25314 |
55 59.21 |
| S | Frag1.F2.1 Frag1.R1.1 |
TTTGTTTTTCTTGTTTTATTGCCAC TAATTTGACTCCTTTGAGCACTGG |
4-28 3810-3787 |
21566-21590 25372-25349 |
57.74 60.5 |
| S | Frag1.F3.1 Frag1.R3.1 |
TGTTTGTTTTTCTTGTTTTATTGCC CAACAGCCCTTGAGACAACTAC |
2-26 3743-3722 |
21564-21588 25305-25284 |
57.47 61.07 |