# 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 TYTGCATRASAAWRR MEME-1 TYTGCATRASAAWRR 3.9e-373 1.5e-374 -860.73 0.0 62 196 2311 3511 0.31633 1.6e-376 97 2 CATRABAA DREME-1 CATRACAA 5.0e-236 2.0e-237 -545.01 0.0 67 203 1044 1360 0.33005 2.0e-239 101 2 ATGYADAT DREME-2 ATGCAAAT 2.5e-101 9.8e-103 -234.88 0.0 81 203 857 1211 0.39901 9.7e-105 101 2 ATGYWAA DREME-3 ATGCWAA 1.8e-104 7.1e-106 -242.12 0.0 78 204 1154 1804 0.38235 7.0e-108 101 2 CCTGSDG DREME-4 CCTGSDG 1.1e-003 4.2e-005 -10.07 0.0 112 204 947 1550 0.54902 4.2e-007 101 2 ATNACAAW DREME-5 ATNACAAW 2.5e-192 1.0e-193 -444.40 0.0 59 203 933 1370 0.29064 9.9e-196 101 2 ATGCGCAT DREME-6 ATGCGCAT 7.5e-035 3.0e-036 -81.79 0.0 63 203 125 152 0.31034 3.0e-038 101 2 CTGTGD DREME-9 CTGTGD 4.1e0000 1.6e-001 -1.82 0.0 161 205 1539 1893 0.78537 1.7e-003 102 2 ATGAATAW DREME-10 ATGAATAW 3.0e-018 1.2e-019 -43.57 0.0 53 203 129 231 0.26108 1.2e-021 101 2 ACAAAGV DREME-11 ACAAAGV 2.0e-023 8.1e-025 -55.47 0.0 102 204 751 1143 0.50000 8.0e-027 101 2 GGAATGY DREME-13 GGAATGY 5.2e-001 2.1e-002 -3.87 0.0 158 204 391 464 0.77451 2.1e-004 101 2 CAWATGAA DREME-14 CAWATGAA 2.7e-025 1.1e-026 -59.78 0.0 79 203 201 281 0.38916 1.1e-028 101 2 GAAATGYA DREME-15 GAAATGCA 1.3e-003 5.3e-005 -9.85 0.0 75 203 130 247 0.36946 5.2e-007 101 2 TKTAAATR DREME-16 TKTAAATR 3.6e-001 1.4e-002 -4.25 0.0 75 203 199 437 0.36946 1.4e-004 101 2 ATTAVCA DREME-17 ATTAVCA 4.0e-012 1.6e-013 -29.46 0.0 60 204 317 734 0.29412 1.6e-015 101 ## # 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).