Table 3

Summary of RIP mutation in the repeat families of S. nodorum strain SN15.

RIP Dominance Scores

NCBI NR Protein Blastx

GIRI Repbase Tblastx


Repeat Family

Copy Number

Full Length (bp)

RIP dominance by highest G:C content [20]

RIP dominance by majority consensus

RIP dominance by deRIP consensus

Hits to deRIP consensus

Hits to majority consensus

deRIP Improve-ment factor (Maximum value)

Hits to deRIP consensus

Hits to majority consensus

deRIP Improve-ment factor (Maximum value)


R8

48

9143

2.96

1.95

2.91

126

77

1.96

R10

59

1241

1.91

0.96

2.07

3

2

2.13

0

3

X0

76

3862

2.13

0.97

2.05

1

0

3

1

1.34

R9

72

4108

1.88

0.92

1.77

250

25

2.75

124

4

1.28

Molly

40

1862

1.21

0.64

1.73

250

161

3.78

34

15

1.92

X3

213

9364

0.63

0.81

1.62

11

10

2.8

X35

19

1157

1.5

1.34

1.43

1

0

X96

14

308

0.87

0.89

1.39

X48

22

265

1.82

1.16

1.33

R22

23

678

1.2

0.84

1.28

2

2

1.06

X26

38

4628

1.16

1.08

1.19

57

57

1.38

Pixie

28

1845

0.77

0.57

1.06

250

190

1.79

17

18

1.25

R37

98

1603

0.49

0.25

0.95

0

55

4

18

1.16

R31

23

3031

0.99

0.83

0.9

16

15

1.44

3

7

1.14

X23

29

685

0.45

0.4

0.9

3

3

0.82

X36

10

512

0.89

0.78

0.87

2

1

1.43

Elsa

17

5240

0.86

0.78

0.82

250

231

2.06

65

30

1.44

R51

39

833

0.47

0.31

0.8

0

3

0

3

X11

36

8555

0.83

0.71

0.78

250

250

1.35

250

228

2.18

X12

29

2263

0.67

0.43

0.76

0

1

10

10

1.44

R39

29

2050

0.59

0.28

0.74

173

149

1.54

34

31

1.88

X28

30

1784

0.83

0.59

0.73

R25

23

3320

0.25

0.6

0.65

4

4

1.19

3

1

0.86

X15

37

6231

0.61

0.46

0.61

250

250

1.45

243

217

1.66

R38

25

358

0.2

0.14

0.5


RIP dominance, a measure of the strength of RIP mutation, is reported for all 3 different RIPCAL comparison methods: versus the highest G:C content sequence; versus the alignment 'majority' consensus and; versus the deRIP consensus. Measures of how much the predicted deRIP consensus of a repeat family resembles its original version, hit discovery scores and deRIP improvement factors, are also summarised for comparisons against NCBI NR Proteins via blastx and the GIRI Repbase database of repetitive elements via tblastx.

Hane and Oliver BMC Genomics 2010 11:655   doi:10.1186/1471-2164-11-655

Open Data