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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.