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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