# 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 NYYWTTGTYATGCAAATN MEME-1 NYYWTTGTYATGCAAATN 1.2e-363 4.7e-365 -838.90 0.0 71 193 2441 3424 0.36788 4.9e-367 96 1 GSCSGGRHTYGAACCMGSRACCTTKHGAT MEME-3 GSCSGGRHTYGAACCMGSRACCTTKHGAT 8.5e-003 3.4e-004 -7.99 0.0 106 182 82 103 0.58242 3.8e-006 90 2 CATRABAA DREME-1 CATRACAA 1.2e-235 4.7e-237 -544.17 0.0 67 203 1048 1368 0.33005 4.6e-239 101 2 ATGYADAT DREME-2 ATGCAAAT 2.1e-101 8.5e-103 -235.03 0.0 81 203 856 1209 0.39901 8.4e-105 101 2 AATRACAA DREME-3 AATRACAA 1.3e-018 5.3e-020 -44.38 0.0 65 203 193 335 0.32020 5.3e-022 101 2 ATGYWAA DREME-4 ATGCWAA 2.7e-105 1.1e-106 -244.01 0.0 78 204 1165 1822 0.38235 1.1e-108 101 2 ATGCGCAT DREME-5 ATGCGCAT 7.5e-035 3.0e-036 -81.79 0.0 63 203 125 152 0.31034 3.0e-038 101 2 CAGSWGG DREME-6 CAGSWGG 5.6e-003 2.2e-004 -8.40 0.0 112 204 786 1282 0.54902 2.2e-006 101 2 ACAAWGS DREME-7 ACAAWGS 4.6e-041 1.8e-042 -96.10 0.0 84 204 707 1145 0.41176 1.8e-044 101 2 ATGAATAW DREME-10 ATGAATAW 4.9e-018 2.0e-019 -43.08 0.0 55 203 133 235 0.27094 1.9e-021 101 2 CMCAGS DREME-11 CMCAGS 7.2e-001 2.9e-002 -3.54 0.0 155 205 2027 2582 0.75610 2.9e-004 102 2 CVTTTC DREME-13 CMTTTC 1.9e0000 7.4e-002 -2.60 0.0 77 205 738 1790 0.37561 7.6e-004 102 2 ATTCAWAT DREME-14 ATTCAWAT 7.2e-019 2.9e-020 -44.99 0.0 101 203 187 233 0.49754 2.9e-022 101 2 CCTGBAG DREME-16 CCTGSAG 7.7e0000 3.1e-001 -1.17 0.0 164 204 653 776 0.80392 3.7e-003 101 2 GTAMTTA DREME-17 GTAMTTA 1.5e-001 6.2e-003 -5.09 0.0 102 204 121 188 0.50000 6.1e-005 101 2 ASAATAG DREME-21 ASAATAG 4.2e-009 1.7e-010 -22.52 0.0 78 204 221 398 0.38235 1.6e-012 101 ## # 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).