| Primer | Sequence (5' to 3') | Component specificity | Position1 |
| BT80-F1 | GCATCCAACGGCCCATA | 2 | 1018-1002 |
| BT80-R3 | CCTAATCCTGTCAAGGA | 2 | 266-282 |
| BT3V1-EXP | *TAGATCCATGGTCAGACAAGAAA | 3 | 217-228 |
| BT3C1-EXP | *ATAAAGCTTTCAAACATGATATGT | 3 | 740-726 |
| BT4V3.17 | ATGGCATTAACAACAGA | 4 | 279-295 |
| BT4C2.17 | GAACATAGGTCCAGCGT | 4 | 629-613 |
| BT129V3.17 | GTTATCATGGCATCGAC | 5 | 639-655 |
| BT129C1.17 | GGACCCTACGTTGCCAG | 5 | 993-977 |
| BTP2F1.17 | TATTAGTAACAGCAACA | 6 | 667-683 |
| BTP2R1.17 | CTAACTTCCATGTCTCT | 6 | 666-650 |
1: Position refers to the nucleotide number within each BBTV DNA component using the numbering system of Burns et al. (1995).
*: The 5' end sequences in bold were non-complimentary linker DNA arms.