# 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 MATTTGCATRWSAAW MEME-1 MATTTGCATRWSAAW 1.6e-215 4.5e-217 -498.15 0.0 64 196 6396 14066 0.32653 4.7e-219 97 2 ATGYADAT DREME-1 ATGYAAAT 4.0e-097 1.1e-098 -225.53 0.0 73 203 2364 4604 0.35961 1.1e-100 101 2 MATRACAA DREME-2 MATRACAA 4.4e-158 1.2e-159 -365.89 0.0 61 203 1789 3420 0.30049 1.2e-161 101 2 CTGKGD DREME-3 CTGKGD 5.2e-004 1.5e-005 -11.11 0.0 107 205 11909 22087 0.52195 1.5e-007 102 2 TATGCWAA DREME-6 TATGCWAA 2.8e-065 7.9e-067 -152.21 0.0 77 203 1131 1969 0.37931 7.8e-069 101 2 CTSCWG DREME-7 CTSCWG 4.5e-009 1.3e-010 -22.77 0.0 77 205 6856 17068 0.37561 1.3e-012 102 2 ATGCGCAT DREME-8 ATGCGCAT 2.3e-045 6.5e-047 -106.35 0.0 71 203 271 374 0.34975 6.5e-049 101 2 CCRCCNC DREME-9 CCRCCHC 3.3e-001 9.6e-003 -4.65 0.0 20 204 729 6505 0.09804 9.5e-005 101 2 ATGHTAAT DREME-11 ATGHTAAT 1.1e-018 3.1e-020 -44.93 0.0 109 203 1177 1814 0.53695 3.0e-022 101 2 AGRKGGCG DREME-14 AGRGGGCG 3.7e-011 1.1e-012 -27.58 0.0 85 203 584 1094 0.41872 1.0e-014 101 2 ACARWG DREME-17 ACARWG 2.0e-015 5.7e-017 -37.41 0.0 99 205 8857 17143 0.48293 5.5e-019 102 2 RAATR DREME-18 GAATR 5.9e-001 1.7e-002 -4.08 0.0 72 206 10547 29334 0.34951 1.7e-004 102 2 CCACCAKG DREME-21 CCACCAKG 6.9e-002 2.0e-003 -6.23 0.0 155 203 783 956 0.76355 1.9e-005 101 2 CCYGGS DREME-22 CCYGGC 8.1e-002 2.3e-003 -6.07 0.0 137 205 8368 12205 0.66829 2.3e-005 102 2 CHGYG DREME-24 CWGYG 1.3e-005 3.7e-007 -14.82 0.0 98 206 12779 25884 0.47573 3.6e-009 102 2 TATGCABA DREME-27 TATGCASA 3.3e-028 9.4e-030 -66.84 0.0 71 203 620 1204 0.34975 9.3e-032 101 2 CAGAKGCC DREME-29 CAGAKGCC 1.0e0000 2.9e-002 -3.54 0.0 93 203 459 888 0.45813 2.9e-004 101 2 CCACTAGR DREME-30 CCACTAGR 1.4e-001 4.1e-003 -5.49 0.0 165 203 523 598 0.81281 4.1e-005 101 2 AYAAAAG DREME-31 AYAAAAG 2.6e0000 7.4e-002 -2.61 0.0 62 204 1436 4404 0.30392 7.6e-004 101 ## # 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).