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Table 2 Results of In silico CpG analyses

From: CpG DNA analysis of bacterial STDs

Genome

CpG hexamere deviation from expected values in %a

Bacteria

Strain

Size (Mb)

G + C%

CpG per kbb

Total CpGc

Stimulatoryd

Inhibitorye

CpG indexf

H. ducreyi

HP35000

1.7

38.2

41.0

112.2

124.8

110.4

6.6

C. trachomatis

E/11023

1.04

41.3

33.8

79.3

90.7

79.1

3.1

C. trachomatis

E/150

1.04

41.3

33.8

79.3

90.8

79.1

3.1

C. trachomatis

E/SW3

1.05

41.3

33.8

79.3

90.8

79.1

3.1

C. trachomatis

L2b/UCH-1

1.04

41.3

33.9

79.4

86.7

76.1

2.9

N. gonorrhoeae

FA 1090

2.15

52.7

92.2

132.9

83.9

143.5

−73.1

N. gonorrhoeae

NCCP11945

2.24

52.4

90.7

132.3

80.3

145.8

−78.6

N. gonorrhoeae

TCDC-NG08107

2.19

52.5

91.7

132.8

80.5

145.8

−79.5

T. pallidum

Dal-1

1.14

52.8

75.1

107.8

107.5

85.7

17.7

T. pallidum

SS14

1.14

52.8

75.0

107.7

107.5

85.6

17.7

T. pallidum

Chicago

1.14

52.8

75.1

107.8

107.6

85.7

17.7

T. pallidum

Mexico

1.14

52.8

75.1

107.8

107.5

85.7

17.7

M. genitalium

G37

0.58

31.7

9.7

38.8

74.9

35.0

1.5

M. genitalium

M2288

0.58

31.7

9.8

38.9

75.0

35.2

1.5

M. genitalium

M2321

0.58

31.7

9.8

39.1

75.3

35.5

1.5

M. genitalium

M6282

0.58

31.7

9.8

39.1

74.4

35.5

1.5

M. genitalium

M6320

0.58

31.7

9.8

38.9

75.0

35.3

1.5

G. vaginalis

409-05

1.62

42.0

48.3

109.3

125.5

87.3

20.2

G. vaginalis

ATCC 14019

1.67

41.4

45.0

105.2

138.7

83.3

26.2

G. vaginalis

HMP 9231

1.73

41.2

44.4

104.7

137.3

83.1

25.2

M. hominis

ATCC 23144

0.67

27.1

12.8

69.4

113.1

70.0

3.8

U. urealyticum

ATCC 33699

0.87

25.8

13.8

82.9

138.2

64.3

8.4

E. coli

ABU 83972

5.13

50.6

49.2

111.7

146.6

108.2

21.1

L. crispatus

ST1

2.04

36.9

27.5

80.8

96.6

80.0

3.7

L. gasseri

ATCC 33323

1.89

35.3

23.4

75.4

99.0

73.0

4.6

  1. aDeviations in amounts of CpG hexameres compared to the expected amount based on GC content
  2. bCpG hexameres occurring per 1 kb of DNA
  3. cTotal number of CpG hexameres compared to the expected amount
  4. dNumber of stimulatory CpG hexameres (RRCGYY) compared to expected amount
  5. eNumber of inhibitory CpG hexameres (NCCGNN and NNCGRN) compared to the expected amount
  6. fIndex calculated from the difference between stimulatory deviation and inhibitory deviation indices, multiplied by the total CpG index, normalized by multiplying with the amount of CpG hexameres per 1 kb