Table 1.
Primer pairs by sequence order.
| Primer Name | Sequence 5′–3′ | Location | Size (bp) | Multiplex Pool | |
|---|---|---|---|---|---|
| Start | End | ||||
| SARS-CoV-2_1_F | GTGTGACCGAAAGGTAAGATGG | 248 | 269 | 956 | 1 |
| SARS-CoV-2_1_R | TTGCATTCATTTGGTGACGC | 1203 | 1184 | ||
| SARS-CoV-2_2_F | GGTGTATACTGCTGCCGTGA | 944 | 963 | 1213 | 2 |
| SARS-CoV-2_2_R | GCCAATCAAGGACGGGTTTG | 2156 | 2137 | ||
| SARS-CoV-2_3_F | CCGCACTCTTGAAACTGCTC | 1912 | 1931 | 1254 | 3 |
| SARS-CoV-2_3_R | GCAGAAGTGGCACCAAATTC | 3165 | 3146 | ||
| SARS-CoV-2_4_F | ACACCACTGGGCATTGATTTAG | 2936 | 2957 | 1264 | 4 |
| SARS-CoV-2_4_R | TTTCAGTAGTGCCACCAGCC | 4199 | 4180 | ||
| SARS-CoV-2_5_F | CTTCATCCAGATTCTGCCAC | 4052 | 4071 | 1296 | 5 |
| SARS-CoV-2_5_R | AGCAGGTGGATTAAACTTCAACTC | 5347 | 5324 | ||
| SARS-CoV-2_6_F | CAACATTAACCTCCACACGC | 4990 | 5009 | 1189 | 6 |
| SARS-CoV-2_6_R | ATCAATAGCCACCACATCACC | 6178 | 6158 | ||
| SARS-CoV-2_7_F | AGAAACCTGCTTCAAGAGAGC | 6108 | 6128 | 1373 | 1 |
| SARS-CoV-2_7_R | ATTACAACCGTCTACAACATGCAC | 7480 | 7457 | ||
| SARS-CoV-2_8_F | GTCACTATTGCAACCTACTGTAC | 7091 | 7113 | 1093 | 2 |
| SARS-CoV-2_8_R | CTTGCCGAGCTGCTGAAATA | 8183 | 8164 | ||
| SARS-CoV-2_9_F | AATCAGCGTCTGTTTACTACAGTC | 7929 | 7952 | 1192 | 3 |
| SARS-CoV-2_9_R | GTGTCAGGGCGTAAACTTTC | 9120 | 9101 | ||
| SARS-CoV-2_10_F | TTGTCGTGCCTGGTTTGC | 8856 | 8873 | 1303 | 4 |
| SARS-CoV-2_10_R | ACGTCATCAAGCCAAAGACC | 10158 | 10139 | ||
| SARS-CoV-2_11_F | AGTGGAGCAATGGATACAAC | 9917 | 9936 | 1239 | 5 |
| SARS-CoV-2_11_R | AGCTACAGTGGCAAGAGAAG | 11209 | 11190 | ||
| SARS-CoV-2_12_F | AGGGTACACACCACTGGTTG | 10995 | 11014 | 1185 | 6 |
| SARS-CoV-2_12_R | CACCATTAGCAACAGCCTGC | 12179 | 12160 | ||
| SARS-CoV-2_13_F | GTGAAGAAATGCTGGACAACAG | 12057 | 12078 | 1180 | 1 |
| SARS-CoV-2_13_R | GCACCACCAAAGGATTCTTG | 13236 | 13217 | ||
| SARS-CoV-2_14_F | TAGTTTAGCTGCCACAGTACG | 12997 | 13017 | 1200 | 2 |
| SARS-CoV-2_14_R | AGTTAAAGCCCTGGTCAAGG | 14196 | 14177 | ||
| SARS-CoV-2_15_F | ATACGCCAACTTAGGTGAACG | 13962 | 13982 | 1284 | 3 |
| SARS-CoV-2_15_R | AACATGTTGTGCCAACCACC | 15245 | 15226 | ||
| SARS-CoV-2_16_F | TGAGTTATGAGGATCAAGATGCAC | 14996 | 15019 | 1243 | 4 |
| SARS-CoV-2_16_R | GCCTGTAAGACTGTATGCGG | 16238 | 16219 | ||
| SARS-CoV-2_17_F | CCCAGATCCATCAAGAATCCTAG | 15933 | 15955 | 1214 | 5 |
| SARS-CoV-2_17_R | TGCGAGCAGAAGGGTAGTAG | 17146 | 17127 | ||
| SARS-CoV-2_18_F | AAGGTGACTATGGTGATGCTG | 16841 | 16861 | 1336 | 6 |
| SARS-CoV-2_18_R | GGTATGCCAGGTATGTCAACAC | 18176 | 18155 | ||
| SARS-CoV-2_19_F | ACTCAAACCACTGAAACAGCTC | 17875 | 17896 | 1239 | 1 |
| SARS-CoV-2_19_R | GTCACTACAAGGCTGTGCATC | 19113 | 19093 | ||
| SARS-CoV-2_20_F | AGCTAGTTGTGATGCAATCATGAC | 18846 | 18869 | 1235 | 2 |
| SARS-CoV-2_20_R | CTTGTTTGGGACCTACAGATGG | 20098 | 20077 | ||
| SARS-CoV-2_21_F | TTTGGGTGTGGACATTGCTG | 19842 | 19861 | 1323 | 3 |
| SARS-CoV-2_21_R | ATAGCCACGGAACCTCCAAG | 21164 | 21145 | ||
| SARS-CoV-2_22_F | TAAGACAGTGGTTGCCTACG | 20912 | 20931 | 1125 | 4 |
| SARS-CoV-2_22_R | TCTGAACTCACTTTCCATCCAAC | 22036 | 22014 | ||
| SARS-CoV-2_23_F | TTCGAAGACCCAGTCCCTAC | 21895 | 21914 | 1405 | 5 |
| SARS-CoV-2_23_R | TGGATCACGGACAGCATCAG | 23299 | 23280 | ||
| SARS-CoV-2_24_F | TTGAACTTCTACATGCACCAGC | 23106 | 23127 | 1111 | 6 |
| SARS-CoV-2_24_R | CCAGAAGTGATTGTACCCGC | 24216 | 24197 | ||
| SARS-CoV-2_25_F | TTGCTGCTAGAGACCTCATTTG | 24093 | 24114 | 1190 | 1 |
| SARS-CoV-2_25_R | GCAACTGGTCATACAGCAAAG | 25282 | 25262 | ||
| SARS-CoV-2_26_F | GGTGACATCTCTGGCATTAATGC | 25061 | 25083 | 1163 | 2 |
| SARS-CoV-2_26_R | TGCTTACAAAGGCACGCTAG | 26223 | 26204 | ||
| SARS-CoV-2_27_F | ACCAGCTGTACTCAACTCAATTG | 26027 | 26049 | 1137 | 3 |
| SARS-CoV-2_27_R | CTGCTACTGGAATGGTCTGTG | 27163 | 27143 | ||
| SARS-CoV-2_28_F | TGACCAGACCGCTTCTAGAAAG | 26908 | 26929 | 1180 | 4 |
| SARS-CoV-2_28_R | GCCTCATCCACGCACAATTC | 28087 | 28068 | ||
| SARS-CoV-2_29_F | TGTCACGCCTAAACGAACATG | 27876 | 27896 | 1147 | 5 |
| SARS-CoV-2_29_R | GATTTCTTAGTGACAGTTTGGCC | 29022 | 29000 | ||
| SARS-CoV-2_30_F | CGAATTCGTGGTGGTGACG | 28550 | 28568 | 1173 | 6 |
| SARS-CoV-2_30_R | GGTGGCTCTTTCAAGTCCTC | 29722 | 29703 | ||