Table 2.
Intergenic primers
| Primer1 | Sequence | Strand2 | Notes3 |
|---|---|---|---|
| 1R | CGAAGATAAGTAATTGGT | AS | ~300 bp 5'of each D1 gene |
| 2F | GTTCTGTTTTTAGTACCG | S | RC of 12R, located ~2.2 kb 3' of all D1 genes |
| 6F | TTGAGAGCTCGTCACGTG | S | ~900 bp 3' of the D1-b gene |
| 7F | TGCAATCATTTTACATATTACTGGTT | S | ~800 bp 3' of the A2 gene |
| 9F | GGGATTACATACCATACCGCA | S | ~1 kb 3' of the B8 gene |
| 11F | ATCCTTTGAAACAGCCCCTC | S | RC of 10R, located ~2.4 kb 3' of the D1-y gene |
| 13F | TGGGAAATACTGACTGCC | S | RC of 5R, located ~2.7 kb 3' of the E2 gene |
| 17F4 | TTTCCAATGTCCTTATTTACGACTTATA | S | qPCR primer with 18R1 |
| 21F | AATGTATTCGGCAGCGAGGT | S | ~1 kb 3' of the D1 genes |
| 5R | GGCAGTCAGTATTTCCCA | AS | RC of 13F, located ~1.1 kb 5' of the D1-b gene |
| 8R | AAGCCTGCTGCTCAATCATC | AS | ~1.2 kb 5' of the A2 gene |
| 10R | GAGGGGCTGTTTCAAAGGAT | AS | RC of 11F, located ~1.1 kb 5' of the B8 gene |
| 12R | CGGTACTAAAAACAGAAC | AS | RC of 2F, located ~1 kb 5' of all D1 genes |
| 14R | AAGTGGTGGTAGGCTCAGTAGTA | AS | ~700 bp 5' of the E2 gene |
| 18R4 | ATGATTCACAGGTTTGTTGCCTC | AS | qPCR primer with 17F1 |
1F, forward; R, reverse
2S = sense; AS = antisense
3RC = reverse complement
4These primers amplify a unique region used to quantify the copy number of BAC plasmids in qPCR reactions.