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Table 1 Most significant dyads detected in promoters of the 53 Gamma-proteobacterial orthologs of lexA.

From: Evaluation of phylogenetic footprint discovery for predicting bacterial cis-regulatory elements and revealing their evolution

Dyad sequence

Dyad identifier

obs_occ

expected_freq

exp_occ

occ_P

occ_E

occ_sig

rank

ctgn{10}cag

ctgn{10}cag|ctgn{10}cag

45

0.0002971522775

1.88

6.2e-45

2.4e-40

39.62

1

ctgn{9}aca

ctgn{9}aca|tgtn{9}cag

47

0.0005035119746

3.19

2.1e-37

8.2e-33

32.08

2

ctgn{8}tac

ctgn{8}tac|gtan{8}cag

36

0.0003516501339

2.26

2.7e-30

1.1e-25

24.98

3

actn{11}cag

actn{11}cag|ctgn{11}agt

38

0.0004247904187

2.66

4.5e-30

1.7e-25

24.76

4

ctgn{1}ata

ctgn{1}ata|tatn{1}cag

43

0.0005681739096

3.83

6.8e-30

2.6e-25

24.58

5

actn{10}aca

actn{10}aca|tgtn{10}agt

39

0.0004770216061

3.02

2.6e-29

9.8e-25

24.01

6

atan{0}cag

atan{0}cag|ctgn{0}tat

39

0.0004971628517

3.38

1e-27

3.9e-23

22.41

7

tgtn{8}aca

tgtn{8}aca|tgtn{8}aca

31

0.0002748483967

1.76

1.6e-27

6.0e-23

22.22

8

atan{6}cag

atan{6}cag|ctgn{6}tat

40

0.0005662014535

3.68

2.5e-27

9.7e-23

22.01

9

tatn{0}aca

tatn{0}aca|tgtn{0}ata

37

0.0005149051727

3.50

4.2e-25

1.6e-20

19.79

10

ctgn{7}ata

ctgn{7}ata|tatn{7}cag

33

0.0005399616828

3.48

5e-21

1.9e-16

15.71

11

gtan{7}aca

gtan{7}aca|tgtn{7}tac

29

0.0003877441875

2.50

5.6e-21

2.2e-16

15.66

12

atan{1}aca

atan{1}aca|tgtn{1}tat

38

0.0007529946923

5.07

1.2e-20

4.7e-16

15.32

13

atan{2}cag

atan{2}cag|ctgn{2}tat

34

0.0006478755931

4.32

3.2e-19

1.2e-14

13.90

14

ctgn{3}ata

ctgn{3}ata|tatn{3}cag

32

0.0006173317980

4.10

4.2e-18

1.6e-13

12.79

15

atan{0}tac

atan{0}tac|gtan{0}tat

30

0.0005247295752

3.57

5.5e-18

2.1e-13

12.67

16

actn{0}gta

actn{0}gta|tacn{0}agt

26

0.0003805581878

2.59

1.4e-17

5.2e-13

12.28

17

tatn{2}aca

tatn{2}aca|tgtn{2}ata

34

0.0008118555000

5.42

2.4e-16

9.2e-12

11.04

18

tatn{6}aca

tatn{6}aca|tgtn{6}ata

32

0.0007321348527

4.75

2.8e-16

1.1e-11

10.97

19

gtan{2}tac

gtan{2}tac|gtan{2}tac

17

0.0001436260620

0.96

7.1e-16

2.7e-11

10.56

20

  1. The table only displays the 20 dyads having a sig ≥ 10 using the TAXFREQ background model. Column content: (1) dyad; (2) dyad identifier (the dyad + its reverse complement); (3) observed number of occurrences (obs_occ); (4) expected frequency (exp_freq); (5) expected number of occurrences (exp_occ); (6) P-values (occ_P), (7) E-value (occ_E), significance (occ_sig), rank.