Table 5.
PCR primers used to validate the presence of breakpoints detected by fingerprints
| Left primer | Right primer | |||||||
| Primer transform | Sequence | Position | Sequence | Position | ||||
| Chr | Start (bp) | End (bp) | Chr | Start (bp) | End (bp) | |||
| M0092D11 | ||||||||
| ar+ br+ | TGCTAAATTTCCCAAGTGCC | 20 | 45,794,352 | 45,794,371 | CCGTCCTCTTAGCGAACTTG | 20 | 46,968,304 | 46,968,323 |
| ar+ br- | TGCTAAATTTCCCAAGTGCC | 20 | 45,794,352 | 45,794,371 | AATTTCAAAATGCGTCTGGG | 20 | 46,968,631 | 46,968,650 |
| ar+ bl+ | TGCTAAATTTCCCAAGTGCC | 20 | 45,794,352 | 45,794,371 | TGACACGCAGGGTAGATCAG | 20 | 46,923,060 | 46,923,079 |
| ar+ bl- | TGCTAAATTTCCCAAGTGCC | 20 | 45,794,352 | 45,794,371 | TCCAACAGGAAGGAGTACCG | 20 | 46,922,743 | 46,922,762 |
| al+ br+ | CTCTCTTTTGTGGGACGAGC | 20 | 45,718,752 | 45,718,771 | CCGTCCTCTTAGCGAACTTG | 20 | 46,968,304 | 46,968,323 |
| al+ br- | CTCTCTTTTGTGGGACGAGC | 20 | 45,718,752 | 45,718,771 | AATTTCAAAATGCGTCTGGG | 20 | 46,968,631 | 46,968,650 |
| al+ bl+ | CTCTCTTTTGTGGGACGAGC | 20 | 45,718,752 | 45,718,771 | TGACACGCAGGGTAGATCAG | 20 | 46,923,060 | 46,923,079 |
| al+ bl- | CTCTCTTTTGTGGGACGAGC | 20 | 45,718,752 | 45,718,771 | TCCAACAGGAAGGAGTACCG | 20 | 46,922,743 | 46,922,762 |
| M0107O02 | ||||||||
| br+ ar+ | AATAGAAGCCAGGCATGGTG | 20 | 48,861,156 | 48,861,175 | GTTAGGAGGAGGGTGGAACC | 17 | 56,663,181 | 56,663,200 |
| br+ ar- | AATAGAAGCCAGGCATGGTG | 20 | 48,861,156 | 48,861,175 | TAGCCGTTCTGACTGGTGTG | 17 | 56,663,261 | 56,663,280 |
| br+ al+ | AATAGAAGCCAGGCATGGTG | 20 | 48,861,156 | 48,861,175 | TAGCTGGGATTACAGGTGCC | 17 | 56,646,379 | 56,646,398 |
| br+ al- | AATAGAAGCCAGGCATGGTG | 20 | 48,861,156 | 48,861,175 | ACAACCTGTCCGACCAGAAC | 17 | 56,646,305 | 56,646,324 |
| M0141F19 | ||||||||
| ar+ cr+ | GGACAGAGGCTTTTGTAGCG | 17 | 56,687,628 | 56,687,647 | ACCACGTAGACAAAGACGGG | 20 | 59,173,964 | 59,173,983 |
| ar+ cr- | GGACAGAGGCTTTTGTAGCG | 17 | 56,687,628 | 56,687,647 | TTCTGGATTCTCCTTGGTGC | 20 | 59,173,950 | 59,173,969 |
| ar+ cl+ | GGACAGAGGCTTTTGTAGCG | 17 | 56,687,628 | 56,687,647 | ATTTGGTTCCTGGTGAGTGC | 20 | 59,153,746 | 59,153,765 |
| ar+ cl- | GGACAGAGGCTTTTGTAGCG | 17 | 56,687,628 | 56,687,647 | AGAAGAACCCGACGACATTG | 20 | 59,153,849 | 59,153,868 |
| br+ cr+ | TATCCTTCAGGAATCGCCAC | 20 | 53,542,992 | 53,543,011 | ACCACGTAGACAAAGACGGG | 20 | 59,173,964 | 59,173,983 |
| br+ cr- | TATCCTTCAGGAATCGCCAC | 20 | 53,542,992 | 53,543,011 | TTCTGGATTCTCCTTGGTGC | 20 | 59,173,950 | 59,173,969 |
| br+ cl+ | TATCCTTCAGGAATCGCCAC | 20 | 53,542,992 | 53,543,011 | ATTTGGTTCCTGGTGAGTGC | 20 | 59,153,746 | 59,153,765 |
| br+ cl- | TATCCTTCAGGAATCGCCAC | 20 | 53,542,992 | 53,543,011 | AGAAGAACCCGACGACATTG | 20 | 59,153,849 | 59,153,868 |
Primer sequence is the appropriately transformed (reversed, complemented, reverse-complemented) primer sequence to test a specific order/orientation of clone regions within the insert. Products were detected for reactions where the primer transform field is in bold. Primer combinations (e.g. ar+ br+) correspond to order and orientation of putative rearrangement and are described in detail in Additional data file 1.