# WARNING: this file is not sorted! # db id alt consensus E-value adj_p-value log_adj_p-value bin_location bin_width total_width sites_in_bin total_sites p_success p-value mult_tests 1 ATTTGCATAACAAWRR MEME-1 ATTTGCATAACAAWRR 4.2e-390 1.9e-391 -899.67 0.0 63 195 2453 3690 0.32308 1.9e-393 97 1 CCATCTATTCTCTCTGARGSCTGCTACCT MEME-2 CCATCTATTCTCTCTGARGSCTGCTACCT 5.0e0000 2.3e-001 -1.49 0.0 108 182 47 61 0.59341 2.8e-003 90 2 CATDABAA DREME-1 CATRACAA 7.2e-258 3.3e-259 -595.18 0.0 61 203 1199 1693 0.30049 3.2e-261 101 2 ATGYWAAT DREME-2 ATGCAAAT 3.7e-071 1.7e-072 -165.26 0.0 81 203 789 1193 0.39901 1.7e-074 101 2 AWATGCR DREME-3 AWATGCA 1.4e-070 6.2e-072 -163.97 0.0 56 204 613 1162 0.27451 6.1e-074 101 2 ATVACAAW DREME-4 ATVACAAW 2.8e-184 1.3e-185 -425.75 0.0 73 203 999 1325 0.35961 1.2e-187 101 2 CCTGSWG DREME-5 CCTGSWG 1.0e-004 4.8e-006 -12.26 0.0 112 204 821 1319 0.54902 4.7e-008 101 2 CTGKGR DREME-7 CTGKGR 4.0e0000 1.8e-001 -1.69 0.0 165 205 2210 2673 0.80488 2.0e-003 102 2 ATGCGCAT DREME-9 ATGCGCAT 2.8e-034 1.3e-035 -80.36 0.0 47 203 140 220 0.23153 1.2e-037 101 2 TKTAAA DREME-10 TKTAAA 7.8e0000 3.5e-001 -1.04 0.0 33 205 279 1492 0.16098 4.3e-003 102 2 MTGAATA DREME-11 MTGAATA 2.4e-016 1.1e-017 -39.05 0.0 56 204 233 501 0.27451 1.1e-019 101 2 GRGAR DREME-12 GRGAR 6.4e0000 2.9e-001 -1.23 0.0 186 206 3910 4273 0.90291 3.4e-003 102 2 GGAATGY DREME-13 GGAATGY 7.9e-001 3.6e-002 -3.33 0.0 150 204 410 512 0.73529 3.6e-004 101 2 GTAWTTM DREME-14 GTAWTTM 7.2e0000 3.3e-001 -1.12 0.0 84 204 234 495 0.41176 3.9e-003 101 2 CGAACCCR DREME-15 CGAACCCR 7.7e-002 3.5e-003 -5.66 0.0 73 203 43 72 0.35961 3.5e-005 101 2 AWCAAAGG DREME-16 AWCAAAGG 2.0e-009 8.9e-011 -23.15 0.0 103 203 225 320 0.50739 8.8e-013 101 2 ATCTRCAT DREME-17 ATCTGCAT 3.5e-033 1.6e-034 -77.82 0.0 67 203 242 372 0.33005 1.6e-036 101 2 ACAAWGCC DREME-18 ACAAAGCC 4.2e-006 1.9e-007 -15.46 0.0 73 203 106 184 0.35961 1.9e-009 101 ## # Detailed descriptions of columns in this file: # # db: The name of the database (file name) that contains the motif. # id: A name for the motif that is unique in the motif database file. # alt: An alternate name of the motif that may be provided # in the motif database file. # consensus: A consensus sequence computed from the motif. # E-value: The expected number motifs that would have least one. # region as enriched for best matches to the motif as the reported region. # The E-value is the p-value multiplied by the number of motifs in the # input database(s). # adj_p-value: The probability that any tested region would be as enriched for # best matches to this motif as the reported region is. # By default the p-value is calculated by using the one-tailed binomial # test on the number of sequences with a match to the motif # that have their best match in the reported region, corrected for # the number of regions and score thresholds tested. # The test assumes that the probability that the best match in a sequence # falls in the region is the region width divided by the # number of places a motif # can align in the sequence (sequence length minus motif width plus 1). # When CentriMo is run in discriminative mode with a negative # set of sequences, the p-value of a region is calculated # using the Fisher exact test on the # enrichment of best matches in the positive sequences relative # to the negative sequences, corrected # for the number of regions and score thresholds tested. # The test assumes that the probability that the best match (if any) # falls into a given region # is the same for all positive and negative sequences. # log_adj_p-value: Log of adjusted p-value. # bin_location: Location of the center of the most enriched region. # bin_width: The width (in sequence positions) of the most enriched region. # A best match to the motif is counted as being in the region if the # center of the motif falls in the region. # total_width: The window maximal size which can be reached for this motif: # rounded(sequence length - motif length +1)/2 # sites_in_bin: The number of (positive) sequences whose best match to the motif # falls in the reported region. # Note: This number may be less than the number of # (positive) sequences that have a best match in the region. # The reason for this is that a sequence may have many matches that score # equally best. # If n matches have the best score in a sequence, 1/n is added to the # appropriate bin for each match. # total_sites: The number of sequences containing a match to the motif # above the score threshold. # p_success: The probability of falling in the enriched window: # bin width / total width # p-value: The uncorrected p-value before it gets adjusted to the # number of multiple tests to give the adjusted p-value. # mult_tests: This is the number of multiple tests (n) done for this motif. # It was used to correct the original p-value of a region for # multiple tests using the formula: # p' = 1 - (1-p)^n where p is the uncorrected p-value. # The number of multiple tests is the number of regions # considered times the number of score thresholds considered. # It depends on the motif length, sequence length, and the type of # optimizations being done (central enrichment, local enrichment, # score optimization).