TABLE 1.
MHV-68 primers used for array element synthesis
| Array element | Forward primer (5′) sequence | Reverse primer (3′) sequence | Location (nt positions) | Product size (bp) |
|---|---|---|---|---|
| vtRNA | ACCATTCGATGCAAATG | CTACACATGAAAATCCTGTGAG | 53-1891 | 1,833 |
| M1 | CATGCAGCTGGCCACCTTA | CCACGCAGTATTGTAGCGG | 2022-3028 | 1,005 |
| M2 | ATGAGGTTTCGTTTTCAGGT | AGCACCTTCACTGTTACTCC | 4025-4627 | 602 |
| M3 | CAGCCATGGCCTTCCTATCC | GAGTATCAATGATCCCCAAA | 6051-7282 | 1,231 |
| M4 | TGGGCACCCAGCCTAGATT | AGTGGCCACACACAACCGT | 8413-9611 | 1,198 |
| ORF 4 | GTCAAAAGTGGCACCACCC | GGTGGTACCGTCTGAGTGA | 9993-10918 | 925 |
| ORF 6-5′ | GGACCCGCTGGTTACATCT | CATGCAGGAATCTGGCACG | 11251-12378 | 1,127 |
| ORF 6-3′ | CTGTCTGCCAGCTTCGTGA | GGAGCAGCAGTGAACTGAG | 13381-14480 | 1,099 |
| ORF 7 | CCTCAGCCTGGTACCATAC | ACTCTGTAGGGAGGCGAAC | 14579-15614 | 1,035 |
| ORF 8-5′ | TCTGCTGTGCCACACGCAT | TCTGGTCACTGACGCAGCT | 16567-17609 | 1,042 |
| ORF 8-3′ | CAGAGACACCCTCATGTGG | GGCCACTAGAGGGAAGTTG | 17962-19060 | 1,098 |
| ORF 9-5′ | GTTCAGATTCCAGGCGGAC | CAGTAGGTCCAGGACCAAC | 19561-20719 | 1,158 |
| ORF 9-3′ | GTAGTGGACTTTGCCAGCC | GGTGCTCTGCCAAGTCAGA | 20951-22070 | 1,119 |
| ORF 10 | CTCTGGACCTACCACTGAC | AGTATCTGTCGCCTCGTGG | 22390-23384 | 994 |
| ORF 11 | GCCAACTATGCCTGGAAGC | ACTCAGCTCACCACCTGGA | 23551-24618 | 1,067 |
| K3 | TTGGATCTGCCACCAGCCA | CACCCCAGTCTACAACAGG | 24752-25312 | 560 |
| M5 | TTCTAGCCTGCTCATTGGCC | GGGATTTCCAGGTAGAGGG | 26290-26500 | 210 |
| ORF 17 | GATCATGACAGGCTCCTGC | TTCCTGCCCTCGCTTCATC | 28832-29879 | 1,047 |
| ORF 18 | AATGTCTCCTGGCCTGCAG | ATCTGGTGGGAGGGAAAGG | 29988-30669 | 681 |
| ORF 19 | GCATTCTGCGGCTTTGACC | TGGAAAGAGGGCGGACATG | 31041-32094 | 1,053 |
| ORF 20 | AGGAGCCAAGCAACTGCTC | ATGGTGCCTCCTGCTTCCA | 32272-32869 | 597 |
| ORF 21 | CTATGCAGAGCCAGAGGAG | AAACTCAGCAGCAGCCTCC | 32941-33926 | 985 |
| ORF 22 | TGTTTGTCTGCCCGGTTGG | CGTGAGCTGACTAGTCTGC | 35164-36410 | 1,246 |
| ORF 23 | GTCATCAAGGCCCCATCCT | GCGCATATTTGCGCAGCAC | 37081-38089 | 1,008 |
| ORF 24 | GAAGACTGCTCCTGGGCAT | GGCAGCCCATAGCAAAGAG | 38792-40069 | 1,277 |
| ORF 25-5′ | GAATCTGCAGCAGAGGGAC | GTCCCTCTGCTGCAGATTC | 40335-41490 | 1,155 |
| ORF 25-3′ | TCCTTTTGGCCAGCGACCT | CCACACATCCTGTTCGTCC | 42841-43869 | 1,028 |
| ORF 26 | ATCATGGCATCCAACAGGAA | GAGCTAGAGCCAACAGGTTCCT | 44420-45325 | 905 |
| ORF 27 | GGACCCTACCACTGTTCTG | TAAACATCCCTGGCTGCCG | 45392-45924 | 532 |
| ORF 29b | GCAATCACTGCCTGCCCTT | GGTCACTAGACAGCAGGAC | 46571-47279 | 708 |
| ORF 30 | AAATGTCTGCCCCCGGATG | TTGGCCGCGCTTGCATCTT | 47505-47736 | 231 |
| ORF 31 | GCGGCCTCTTTCTAACCCT | CAGATCGACCAGGAGCTCA | 47751-48359 | 608 |
| ORF 32 | TGAGCTCCTGGTCGATCTG | GGAGAAAGTCCCTCGTGAC | 48341-49420 | 1,079 |
| ORF 33 | CTTTACATGCACCACGTCC | GGTCAGATAGCCTCACGAG | 49677-50509 | 332 |
| ORF 29a | CCGCAGCACAGTTTCCAGT | GTGGCACACATCAAGGTGC | 50577-51425 | 348 |
| ORF 34 | CCGAAGCAGATCCTGTGCT | AATGCTGTCGTGGGTGGCA | 51490-52370 | 380 |
| ORF 35 | GACACGAAACTGCTGGCCA | CCATCGAGCCTCCAACAAG | 52426-52850 | 424 |
| ORF 36 | AGGATGGAGAGGACACTGC | TGGAGTGAACTGCTGCCGT | 52881-54046 | 1,165 |
| ORF 37 | GTTCTGGGAAACATGGCCC | AGGTACTCGTGCAGCACAG | 54180-55496 | 1,316 |
| ORF 39 | TGCCTGCCCTTAAAGTGCC | TTTGCTCTGGGGGGTTGTG | 55839-56950 | 1,111 |
| ORF 40 | GTGCTTCTGCCGCTGGTAA | AAGTCCTTTGGGCCGGATG | 57026-58686 | 1,660 |
| ORF 42 | CATCCTTCCCAGGCTGATG | CATACATCAACCCTGCGCG | 58899-59599 | 700 |
| ORF 43 | GTTTACCAGCTGGGCCAAC | TGGTGGCAGCACCTCTACT | 59634-61118 | 1,484 |
| ORF 44-5′ | AATCACAGGGACTGCTGGG | GGATGGCTGAGGTCTGAGT | 61488-62029 | 541 |
| ORF 44-3′ | GCTGGACTCGCCTCTTTGT | GTTCACTGCTCCTCATGGG | 62303-63559 | 1,256 |
| ORF 45 | CCCGATCTCTCGACCAATA | TCAATCCAACCATGGCCAG | 63652-64225 | 573 |
| ORF 46 | GCCTGGTAACCATGGACAC | GAGGGTTTGTTGTGCTGCG | 64291-65014 | 723 |
| ORF 47 | CCTGGGGCATAGTTCTTTG | GTGTCCATGGTTACCAGGC | 65013-65580 | 567 |
| ORF 48 | AAACCCGTGAAGGTGGTGG | TTCTGCCCAAGGACCATGG | 65636-66560 | 924 |
| ORF 49 | TCTCTGGAAAGCGTGGTCC | TTCTGCAGCGATGGCCTCT | 66750-67619 | 869 |
| ORF 50 | CAGGCATCCATGTGGGTAC | CAGCAGTGTCCTGGTTTGC | 67951-69339 | 1,388 |
| M7 | GCCGAGACTGTAGAGGGTA | GGTCGTATCCAAAGCAGGG | 69571-70841 | 1,270 |
| ORF 52 | CGATGGCGTCCAAAAAGCC | CTGTTTGAGAGGATGGGCC | 71013-71366 | 353 |
| ORF 53 | AATGCAGGTCCTGGTCGTG | AGGTTGTCTCCAGGGCACT | 71402-71702 | 300 |
| ORF 54 | CTCCTTTGTGCCCAAGCAC | TCTGCAGCTTCGTGCGGAA | 71820-72602 | 782 |
| ORF 55 | TGGGAAACCCGGTGTACCT | GTTTGGGTCAAGTGGGGTG | 72681-73287 | 606 |
| ORF 56-5′ | ACACGAGGGCGCAACTGAA | CAACCGTGTTGCTCGTGCA | 73393-74720 | 1,327 |
| ORF 56-3′ | TGCACGAGCAACACGGTTG | CCTCTACACTCGAGCATGC | 74702-75799 | 1,097 |
| M8 | TCCACCAGTTGAGGAGCCA | TCTGGGCGCAGTTTACCAG | 76040-76456 | 416 |
| ORF 57 | GTGCTGACCCACATGCTAG | CCTTGGTGCGGTGTGTTTG | 76650-77139 | 489 |
| ORF 58 | TCAGACGTGTTCCTCCCAC | TCCAGAAAGCAGCCAGCAG | 77323-78239 | 916 |
| ORF 59 | CTTGACACTGAGCGCCTCT | GTAGCTTGGGGCGCTTAGT | 78275-79424 | 1,149 |
| ORF 60 | ACCACGCTGGGTTCCTTGA | GGGTGGAATGAGAGCACAC | 79519-80445 | 926 |
| ORF 61 | CCAAGAAGGCCGAAGTCCT | GTGCAGACAAGAAGCACCC | 80523-81907 | 1,384 |
| ORF 62 | TGCATGCTGGGACTGTCAG | ACTGCCACGGTCCTCTAGA | 82867-84013 | 1,146 |
| ORF 63 | TGCACCTATGCACCCTGGA | CTTGGCTGGCAGCAGACTT | 84061-85104 | 1,043 |
| ORF 64-5′ | TGGCTGGGTTTCGCATCGA | TGGACATGGTCTGCGAGGT | 86586-87978 | 1,392 |
| ORF 64-3′ | TGCACGTGGAAACCCACCA | GTCATGGGTGACACCAGGA | 92721-93790 | 1,069 |
| ORF 65 (M9) | CAGGGTCAAAGCTCCAGCT | GGTCGATTCCCCCAAGTTC | 93992-94508 | 516 |
| ORF 66 | TCTATGGCCACCTCAGTGG | CTCCCTAAATGTCGCCCTC | 94581-95671 | 1,090 |
| ORF 67 | GACGGACATGGCTAACCAG | CTAGTTTACTGGCCAGCGC | 95743-96422 | 679 |
| ORF 68 | CATTGCCCCCCATGACTCA | AGAGCCTGTTGAGCGCATG | 96662-98078 | 1,416 |
| ORF 69 | CATGCGCTCAACAGGCTCT | AGCAGACATTATCGGCCGG | 98060-98850 | 790 |
| ORF 72 | TACACCTGCGACCTCCATG | TGGCAACGAGGAAAGGGCA | 102401-103197 | 796 |
| M11 | TGTTGTGCGTGCGCAGCTA | TTCGCCAGGGCATGCAACA | 103325-103890 | 565 |
| ORF 73 | CACTTGACCCACACCCTTC | GAGACCCTTGTCCCTGTTG | 103932-104930 | 998 |
| ORF 74 | AGCCACGATGCTTGTCCTG | CAAACTGCCCTCCTGACAG | 105050-106054 | 1,004 |
| ORF 75c-5′ | CAAGAACTGGTCCGTCTCG | GTCTTGTGTGGAGAGGCGA | 108896-110020 | 1,124 |
| ORF 75c-3′ | TGACGTGAGCGATGGTGGT | TGCCACTGCCAAGGGAAGA | 106152-107369 | 1,217 |
| ORF 75b-5′ | TCCAAGTCTATGCCAGGGC | CTTGGATGGAGCACCTGAC | 112671-113879 | 1,208 |
| ORF 75b-3′ | CAATGACTCCACAGACGCC | CCATCGGTGGATAGTGTCC | 110081-111129 | 1,048 |
| ORF 75a-5′ | CTCCGAGGTGGATGACAGA | TAACGATGGCTCCAGGACC | 116638-117740 | 1,102 |
| ORF 75a-3′ | CTTGGCCTCGCATGTACCA | TGCTGCCAGTGCCCATAAG | 114041-115420 | 1,379 |