# 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 NATTTGCATRACAAWRR MEME-1 NATTTGCATRACAAWRR 6.0e-313 2.9e-314 -721.96 0.0 64 194 1944 2869 0.32990 3.0e-316 96 1 TRATCWRRRGGTCSYGGGTTCRAGTCCC MEME-3 TRATCWRRRGGTCSYGGGTTCRAGTCCC 1.8e-002 8.6e-004 -7.06 0.0 73 183 55 87 0.39891 9.4e-006 91 2 CATRABAA DREME-1 CATRACAA 1.1e-199 5.0e-201 -461.20 0.0 67 203 872 1130 0.33005 5.0e-203 101 2 ATKCANAT DREME-2 ATGCAAAT 5.5e-085 2.6e-086 -197.06 0.0 69 203 640 982 0.33990 2.6e-088 101 2 ATNACAAW DREME-3 ATNACAAW 5.2e-173 2.5e-174 -399.75 0.0 59 203 808 1168 0.29064 2.4e-176 101 2 ATGCGCAT DREME-4 ATGCGCAT 2.2e-024 1.0e-025 -57.54 0.0 63 203 92 114 0.31034 1.0e-027 101 2 ATGYWAA DREME-5 ATGYWAA 2.2e-082 1.1e-083 -191.06 0.0 80 204 922 1418 0.39216 1.0e-085 101 2 CMCAGS DREME-6 CMCAGS 1.9e-001 8.8e-003 -4.73 0.0 155 205 1754 2220 0.75610 8.7e-005 102 2 CCTTTSW DREME-7 CCTTTSW 1.4e-011 6.8e-013 -28.01 0.0 114 204 750 1116 0.55882 6.8e-015 101 2 RCATTCCW DREME-9 RCATTCCW 2.5e-002 1.2e-003 -6.73 0.0 147 203 249 300 0.72414 1.2e-005 101 2 CAGYAGG DREME-12 CAGCAGG 1.5e-003 7.0e-005 -9.57 0.0 108 204 353 559 0.52941 6.9e-007 101 2 MATGAATA DREME-14 MATGAATA 5.5e-008 2.6e-009 -19.76 0.0 55 203 78 147 0.27094 2.6e-011 101 2 CATTTAM DREME-16 CATTTAM 3.8e0000 1.8e-001 -1.70 0.0 72 204 173 409 0.35294 2.0e-003 101 2 CCTRSAG DREME-17 CCTRSAG 2.6e0000 1.2e-001 -2.10 0.0 162 204 657 785 0.79412 1.3e-003 101 ## # 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).