TABLE 1.
Primer pairs found to be polymorphic in this survey
| Name | Sequencea | Expected size (bp)b | Target repeat(s)c | Position in genomed | Temp (°C)e | No. of variantsf |
|---|---|---|---|---|---|---|
| HCMVTRL8C | F, cccccgagacgagagccaccc | 252 | (GGC)4 | 7287 | 70 | 2 |
| R, ccatcctcgccttcggacgcccc | ||||||
| HCMVUL23C | F, ggtcgcgacgtcttaggagg | 229 | (A)10 | 28762 | 70 | 4 |
| R, cttcccgtttgactcgcgtgc | ||||||
| HCMVUL30C | F, cctccacacgctcagccgc | 282 | (TG)5 | 37254 | 70 | 2 |
| R, gcgccgtcaacagcgtgcc | ||||||
| HCMVUL37C | F, ggcgtcgatgggttcacctcgggcg | 157 | (TTC)4 | 52405 | 60 | 2 |
| R, ggagaccgagcggtcccgtggacttgg | ||||||
| HCMVUL38N | F, gcagcatgtggggctaatagg | 400 | (A)10 | 51083 | 70 | 3 |
| R, gctgcgagccaattcgttgg | ||||||
| HCMVUL46C | F, cctcgcggtttggctttgagc | 138 | (CG)5 | 60374 | 68 | 2 |
| R, cccgcagctgctctatcaac | ||||||
| HCMVUL50C | F, ggcggatgacggtgatgggtcg | 348 | (CTC)4...(GGC)4...(GAG)4 | 72429 | 70 | 3 |
| R, ggcgggaaagcggtcctctcgg | ||||||
| HCMVUL67AN | F, gcctttggtgctcgttgagcc | 280 | (T)10 | 96977 | 63 | 2 |
| R, gtggggacgggaatcgatgtc | ||||||
| HCMVUL67BC | F, gacatcgattcccgtccccac | 303 | (GCG)4 | 97476 | 65 | 2 |
| R, gaggacgaggagacgacgacc | ||||||
| HCMVUL68C | F, gggagggagaggacgtggggctcg | 414 | (T)11 | 97928 | 60 | 7 |
| R, cgctgccagacgcccgattacgagg | ||||||
| HCMVUL69C | F, gcttaacttgatgacgccgtcgcc | 209 | (GGT)5(GGC)4(TGC)3 | 98290 | 65 | 5/9 |
| R, cctcgtaatcgggcgtctggcagcg | ||||||
| HCMVUL95C | F, ggctgagctgtacgtctttgtttgg | 388 | (GGT)5 | 139531 | 60 | 4/4 |
| R, ggcgcagtcttggataacgatgggg | ||||||
| HCMVUL96N | F, cggtttcggcgacgtgcgatttgg | 297 | (A)10 | 140406 | 70 | 3 |
| R, gcgcagcttcgcgcatccactgg | ||||||
| HCMVUL102C | F, cctccaccgcttccaccacc | 167 | (TTC)4 | 148933 | 60 | 2 |
| R, ccgccagcgaacgcaccc | ||||||
| HCMVTRAN1N | F, cccgctaaggacttacc | 397 | (A)11 | 156864 | 55 | 3 |
| R, gctgtaagtctcacctagc | ||||||
| HCMVTRAN2N | F, ccatccgtctagtttttcg | 307 | (TGTA)4 | 157332 | 55 | 2 |
| R, ccaccgtgatagaagacacc | ||||||
| HCMVTRAN3C | F, cctctcctccagtggtagtcgtg | 342 | (TGC)4...(T)10...(TAT)4 | 157835 | 60 | 4/10 |
| R, cctcctctccccatcatcttctcc | ||||||
| HCMVUL111C | F, ccatgatcaattaagcccaccacc | 431 | (GGT)4...(A)10...(A)10...(CGA)4 | 159451 | 62 | 4/5 |
| R, cgtaatcctctggacgacactgcg | ||||||
| HCMVUL112AC | F, ggaggaacagcaacggcagagg | 233 | (GGT)3 | 161192 | 63 | 2 |
| R, ggactcaccgtcgttctcggagg | ||||||
| HCMVUL122N | F, ggctgagaacagtgatcagg | 330 | (AT)5 | 170988 | 60 | 3/5 |
| R, gcgtgacacgtttattgagtagg | ||||||
| HCMVUL123I2N | F, gcacatgggtcacatacaggag | 295 | (A)9 | 172660 | 60 | —/6 |
| R, ggtgctgttaacggtggaggg | ||||||
| HCMVUL123I1N | F, ccctccaccgttaacagcacc | 265 | (TGG)4 | 173066 | 70 | 3 |
| R, gactcatggtcgctcggcag | ||||||
| HCMVUL132C | F, ggaatctgccagctggtgctgttc | 307 | (CCT)4 | 177227 | 65 | 2/2 |
| R, gccggattttgttcctcgagccc | ||||||
| HCMVUS35C | F, gacgaagatgccgatgtgtgac | 325 | (G)12 | 225448 | 65 | —/6 |
| R, cgtagcgtacgcccaacggc |
a
F, forward; R, reverse.
b
Expected length of the PCR fragment in the AD169 genome (GenBank entry HEHCMVCG).
c
Ellipses indicate repeats separated by a stretch of nonrepetitive sequence; contiguous repeats are not separated by ellipses. Repeats in bold are those found within open reading frames according to the GenBank annotation.
d
Nucleotide number of the first repeat within the primer from the same reference sequence.
e
Annealing temperature used for PCR.
f
The number of variant alleles as determined by length analysis and sequencing (number of length variants/number of sequence variants).