TABLE 3.
Primers used to generate PCR amplicons
| Primer name | Sequence | Target fragments/function |
|---|---|---|
| pDual_backbone_Fw | GAGTGATTATCTACCCTGCTTTTGCT | Complete segment |
| pDual_backbone_Rev | GAGTACGACAATTAAAGAAAAATACCCTTGTTTCTACT | Complete segment |
| T7 Seg5 +sense_Fw | TAATACGACTCACTATAGGGAGCAAAAGCAGGGTAGATAATCA | Complete segment |
| T7 Seg5 +sense_Rev | AGTAGAAACAAGGGTATTTTTCTTTAATTGT | Complete segment |
| T7 Seg5 −sense_Fw | AGCAAAAGCAGGGTAGATAATCA | Complete segment |
| T7 Seg5 −sense_Rev | TAATACGACTCACTATAGGGAGTAGAAACAAGGGTATTTTTCTTTAATTGT | Complete segment |
| Seg5_302-329_Fw | GGAAAGATCCTAAGAAAACTGGAGGACC | D |
| Seg5_598-624_Fw | GGAGTTGGAACAATGGTGATGGAATTG | A, B |
| Seg5_755-780_Fw | CAATGATGGATCAAGTGAGAGAGAGC | D, E |
| Seg5_959-986_Fw | GACTGCTTCAAAACAGCCAAGTGTACAG | B, C |
| Seg5_1256-1283_Fw | GCCAAATCAGCATACAACCTACGTTCTC | E |
| Seg5_1565-1528_Rev | AGTAGAAACAAGGGTATTTTTCTTTAATTGTCGTACTC | A, B, C, D, E |
| Seg5_1283-1256_Rev | GAGAACGTAGGTTGTATGCTGATTTGGC | E |
| Seg5_986-959_Rev | CTGTACACTTGGCTGTTTTGAAGCAGTC | B, C |
| Seg5_780-755_Rev | GCTCTCTCTCACTTGATCCATCATTG | D, E |
| Seg5_624-598_Rev | CAATTCCATCACCATTGTTCCAACTCC | A, B |
| Seg5_329-302_Rev | GGTCCTCCAGTTTTCTTAGGATCTTTCC | D |
| Seg5 CpGH amplicon A | CAAAAGCAGGGTAGATAATC | Seg5 serial passage |
| Seg5 CpGH amplicon A | TCGTCACCATTGTTCGCTTG | Seg5 serial passage |
| Seg5 CpGH amplicon B | GCGCGAACTAATACTTTACG | Seg5 serial passage |
| Seg5 CpGH amplicon B | TTACGGCTCTCTCTAACTTG | Seg5 serial passage |
| Seg5 CpGH amplicon C | AAAATTTCAAACCGCGGCGC | Seg5 serial passage |
| Seg5 CpGH amplicon C | TTTGAAGCTATTTGAACGCC | Seg5 serial passage |
| Seg5 CpGH amplicon D | CATAAAAGGAACGAAAGTCC | Seg5 serial passage |
| Seg5 CpGH amplicon D | GTACTCCTCTGCATTGTCTC | Seg5 serial passage |
| IlluminaTag1F | ACACTCTTTCCCTACACGACGCTCTTCCGATCTAACACATCGTAAAACGACGGCCAGT | Deep sequencing |
| IlluminaTag3F | ACACTCTTTCCCTACACGACGCTCTTCCGATCTCCGTATATGTAAAACGACGGCCAGT | Deep sequencing |
| IlluminaTag5F | ACACTCTTTCCCTACACGACGCTCTTCCGATCTGAGATAACGTAAAACGACGGCCAGT | Deep sequencing |
| IlluminaTag8F | ACACTCTTTCCCTACACGACGCTCTTCCGATCTTGCTCCGAGTAAAACGACGGCCAGT | Deep sequencing |
| IlluminaTagR | GACTGGAGTTCAGACGTGTGCTCTTCCGATCTCAGGAAACAGCTATGAC | Deep sequencing |
| Seg5 PR8_F | GTAAAACGACGGCCAGTTCTGCTTTTGACGAAAGGAG | Slippage sequencing |
| Seg5 PR8_R | CAGGAAACAGCTATGACAACCTTGCATCAGAGAGCAC | Slippage sequencing |
| Seg5 CDLR_F | GTAAAACGACGGCCAGTTCTGCTTTTGACGAAAGAAG | Slippage sequencing |
| Seg5 CDLR_R | CAGGAAACAGCTATGACAGCCTTGCATCAGAGAGCAC | Slippage sequencing |
| Reporter GFP_F | AGGGTGACAAAAACATAGGATCC | Slippage sequencing |
| Reporter GFP_R | CAGGGCACGGGCAGCTTGC | Slippage sequencing |
