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Table 1 The typical sites in two-way cleavage scenarios

From: High-throughput sequencing of methylated cytosine enriched by modification-dependent restriction endonuclease MspJI

Typical sites

Fragments' length(bp)

Sites’ number in Arabidopsisgenome

CNNR type

YNCGNR

32

628107

Total 4194480

Symmetrical CGNR

YCHGR

31

840155

Symmetrical CHGR

CHHG

30

2726218

Symmetrical CHHG

CYHAG

29

452582

Total 1169473

Symmetrical CHHRG

CHYAHG

28

385221

Symmetrical CHHRNG

TDDGCHHA

34

168028

symmetrical YNNGCNNR

TDDGNCHHA

35

163642

Symmetrical YNNGNCNNR

Total cytosines in the sites above

Total cytosines in Arabidopsis genome

Generation rate

10727906

42859589

25.03%

  1. The two-way cleavage is caused by the MspJI recognition on the symmetrically methylated sites which are mostly enriched in plant genome. We calculated the typical symmetrical CNNR sites in case of MspJI digestion, and found that these sites contain 10.72 M cytosines which account for 25.03% of the total cytosines in Arabidopsis genome. (R = A or G; Y = C or T; H = A or C or T; D = A or G or T).