# 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 ATTTGCATAWCAAWR MEME-1 ATTTGCATAWCAAWR 7.8e-090 4.9e-091 -207.95 0.0 80 196 1060 1602 0.40816 5.1e-093 97 1 CTATTCTCTCTGAAGSCTGCTACCTGGAG MEME-2 CTATTCTCTCTGAAGSCTGCTACCTGGAG 3.7e0000 2.3e-001 -1.47 0.0 146 182 36 37 0.80220 2.9e-003 90 1 GTCACCTCATTAGCATAAACTCAGGTRTGG MEME-3 GTCACCTCATTAGCATAAACTCAGGTRTGG 6.0e-005 3.7e-006 -12.50 0.0 123 181 44 44 0.67956 4.1e-008 90 2 ATGYWAA DREME-1 ATGYAAA 9.2e-040 5.7e-041 -92.66 0.0 78 204 657 1123 0.38235 5.7e-043 101 2 MATRACAA DREME-2 MATAACAA 2.2e-041 1.4e-042 -96.37 0.0 75 203 324 470 0.36946 1.4e-044 101 2 WTATGCR DREME-3 WTATGCA 2.4e-062 1.5e-063 -144.68 0.0 80 204 497 698 0.39216 1.5e-065 101 2 ACAAWGR DREME-5 ACAAWGR 2.1e-003 1.3e-004 -8.93 0.0 90 204 304 561 0.44118 1.3e-006 101 2 CCTKTGA DREME-7 CCTKTGA 2.2e0000 1.4e-001 -1.98 0.0 94 204 129 229 0.46078 1.5e-003 101 2 ATCTRCAT DREME-8 ATCTRCAT 1.6e-014 9.7e-016 -34.57 0.0 65 203 125 204 0.32020 9.6e-018 101 2 TATTCATR DREME-9 TATTCATG 6.8e-008 4.3e-009 -19.27 0.0 41 203 62 137 0.20197 4.2e-011 101 2 CAGSACC DREME-10 CAGCACC 2.1e0000 1.3e-001 -2.03 0.0 104 204 102 162 0.50980 1.4e-003 101 2 GTGGRGA DREME-11 GTGGRGA 1.0e0000 6.4e-002 -2.74 0.0 4 204 11 159 0.01961 6.6e-004 101 2 CAGCAGG DREME-13 CAGCAGG 2.8e0000 1.7e-001 -1.75 0.0 116 204 120 177 0.56863 1.9e-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).