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.

Krzywinski et al. Genome Biology 2007 8:R224   doi:10.1186/gb-2007-8-10-r224