TABLE 2.

Cloned Cbs junctions: source and conditions for PCR amplification

Cbs name	Source library	Cbs insert size (kb)	Specific primers: SP-G and SP-Cb	Temperaturec	Band sized
1L-1	5′ rDNA	NA	G: TAAAACTAACAACAAAAAGCAA	55°	1.2
C: AACTCAGATTTCATTTTTCAAG
1L-2	3′ rDNA	NA	G: GGGTTTTAACTTATTTTTAA	55°	0.5
C: ATAGCAAATTGTTATATAGA
1L-3	Sau3A	1.1	G: TATAATTCATGAATAAAAGC	55°	1.0
C: AATACTTCTAACTATGAAAG
1L-4	Uni1	1.2	G: ATCCAATATTAGGAACTGAAGC	55°	1.1
C: TTTAATCATCTTAAAACTGAAGC
1L-5a	Uni1	0.6	G: TAAGTGTCATAGCTCCCAAG	60°	0.5 (−)
C: AATTAAGTCTATTATATTAGCAAAAAG
1L-6	Sau3A	1.0	G: TTGATGAAACTTTAACGAGTAA	55°	0.55 (<)
C: TGATTTTAGTTATCAGAATTCATTT
1R-1	Sheared	1.6	G: CAAAAATTCAAAAAGTAGGT	55°	1.55 (<)
(Tt826)	C: GATCAACTTCTGTATGATGTT
1R-2	Sheared	0.85	G: ATAAACCGCTTTTTAACTTTAG	55°	0.7 (>)
C: TCTATTATGTTATTTATGATGTAACG
1R-3a	Sheared	0.3	G: TTTATTATTCTTATTTTTGTAAATTG	55°	0.15
C: AAATATTTTTAAGAGGTTGGTTTe
1R-4	Uni1	1.3	G: AATCTCTTATATATTTTCAACCTTAG	55°	0.9 (<)
C: ACCACAAAAGTAAGTTAAGTACG
1R-5	Uni1	0.8	G: TTTCTTAAGAGTAGGGCTTTAG	55°	0.7 (−)
C: AAATCTTCTTTCTTCCATCTATC
1R-6	Sheared	0.8	G: TGAAATTTGTTAAAATTAAAGGA	55°	0.6
C: TGGATAATTTATAGGTCGTTTC
1R-7	Sheared	0.85	G: TCACTTTTGAACTTACAAGCAA	50°	0.45
C: TTTAATAATAAAAAATATGTTATAAGe
1R-8	Sau3A	0.6	G: AAGCTTAAAAGAAAATTAGTTAAAAA	50°	0.5
C: AGCTACTATTTTATGAGATTACCA
2R-1	Tt814, Tt816	NA	G: CTACATTAAAAATGATAAAA	50°	0.35
C: CATGCATTTTTAATTTTGAG
3L-1	Sau3A	1.15	G: CCTAAGTTAATAGATATTTTG	50°	1.05 (>)
(Tt701)	C: AATAAACTGCACATAAAACT
3L-2	Sheared	0.55	G: AGATTAAACATAAGGATTCAAAC	55°	0.4
(Tt819)	C: TTGGTTATCTTTTAGTAAAGTTTG
3L-3	Sheared	0.8	G: TCAAAATTGGCTTTTAATTTC	50°	0.6
C: AAAATAATTCAAACTCTTCTCAAC
3L-4	Sheared	0.6	G: TTCTGTTATATTATGAATGTGGA	50°	0.45 (−)
C: TCAAGTTTTATCAAACAAAATG
3R-1	Sau3A	0.8	G: GAATTTATATTATTTTAAGTTTCAACCC	55°	0.65
C: AAATTATCTTTTTCTTTTGCTATC
4L-1	Tt835, Tt829	NA	G: TTTATCTATTATTTAAAAAC	45°	0.25
C: CTAACAGTTTAATTAATAAG
4L-2	Sheared	1.3	G: AATAGAATAGCGACCATTAG	55°	1.2
C: ATACTGATTTTTGCAACAAC
4L-3	Sheared	0.9	G: TTTATTCCTAAAAAATTAAAAGTTC	50°	0.7 (>)
C: AAACAAAATTTTAGCATAAAAAG
5-1	Sau3A	0.95	G: CAATAATTTCAAAAAAATGG	55°	0.9 (<)
C: TAAAAAAGCAGGATTACAAT
5-2	Sau3A	1.55	G: GATCCAACTATTAATTATTTCTT	50°	1.3
C: CTTTCTTATTCTGCTTTTCC
5-3	Sheared	0.75	G: TACTAATCTTATGGTTCTTCACAC	60°	0.6 (−)
C: CATGATAAAATGTTATTGTTGTTG
5-4a	Sheared	1.4	G: TTCCTTTTTCATTTAAAGTTTG	60°	1.2
C: TATTATTGATGCTAAAAATTGC
5-5a	Sheared	0.55	G: TGAATAAGCATAGCACCTATTT	55°	0.45
C: AAATTTTGCCTTAGTGTTTCTA
5-6a	Sau3A	0.7	G: AGAAAGTAGCTAACTTCATAAAA	55°	0.65
C: AAAGTAACTAAAAATAATCTCCTTG
5-7	Sau3A	1.8	G: GATCAATAGTTTGACAAATAAAAA	55°	1.7
			C: ATTCATAAAAGTATGCACAATG

Sau3A, Sau3A-digested MIC DNA; Sheared, sheared MIC DNA; Uni1, unisomic 1 Sau3A-digested whole-cell DNA; rDNA, 5′ and 3′ flanks (Yao et al. 1985); Tt-prefixed Cbs, originally characterized by Yao et al. (1987); those reisolated from the Cbs library are in parentheses.

^aA functional variant Cbs element sequence: 1A substitution for Cbs 1L-6, 5-5, and 5-6, and 15A substitution for Cbs 1R-3 and 5-4.

^bSequences are listed 5′–3′; see materials and methods for explanation of G and C designation.

^cPCR annealing temperature; all other Cbs amplification parameters are as described in materials and methods.

^dBand size is the size of the PCR product (in kilobases) from B DNA. For B-C3 polymorphic bands, “>,” “<,” and “−” in parentheses indicate that the C3 band is larger, smaller, or missing, respectively, compared to B.

^eThe primer overlaps the Cbs or lies in the MIC limited sequence immediately adjacent to the Cbs.