# 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 CYWTTGTYATGCAAA MEME-3 CYWTTGTYATGCAAA 3.6e-161 8.7e-163 -373.16 0.0 60 196 5376 12777 0.30612 8.9e-165 97 2 ATGYADAT DREME-1 ATGYAAAT 1.5e-080 3.6e-082 -187.54 0.0 73 203 2151 4256 0.35961 3.5e-084 101 2 MATRACAA DREME-2 MATRACAA 6.0e-141 1.5e-142 -326.59 0.0 61 203 1655 3195 0.30049 1.4e-144 101 2 CTGKGD DREME-4 CTGKGD 7.1e-004 1.7e-005 -10.96 0.0 107 205 11631 21566 0.52195 1.7e-007 102 2 CDGSAG DREME-5 CWGSAG 2.0e-007 4.9e-009 -19.14 0.0 77 205 7116 17824 0.37561 4.8e-011 102 2 ATGNTAAT DREME-8 ATGHTAAT 2.6e-013 6.4e-015 -32.68 0.0 69 203 845 1963 0.33990 6.3e-017 101 2 ATGCGCAT DREME-9 ATGCGCAT 6.9e-038 1.7e-039 -89.28 0.0 71 203 237 332 0.34975 1.7e-041 101 2 AGRKGGCG DREME-12 AGRKGGCG 3.7e-011 9.0e-013 -27.73 0.0 85 203 581 1087 0.41872 8.9e-015 101 2 ACARWG DREME-13 ACARWG 1.5e-011 3.6e-013 -28.66 0.0 99 205 8558 16680 0.48293 3.5e-015 102 2 TATGCAVA DREME-15 TATGCAMA 2.7e-061 6.6e-063 -143.18 0.0 89 203 1322 2125 0.43842 6.5e-065 101 2 RCCTGGS DREME-18 RCCTGGC 1.2e0000 3.0e-002 -3.52 0.0 152 204 4441 5808 0.74510 3.0e-004 101 2 CSGCCKC DREME-23 CSGCCKC 7.8e0000 1.9e-001 -1.66 0.0 22 204 264 2065 0.10784 2.1e-003 101 2 ATAAKAAT DREME-24 ATAAKAAT 9.6e-001 2.3e-002 -3.76 0.0 41 203 278 1134 0.20197 2.3e-004 101 2 CVGGGA DREME-28 CAGGGA 6.4e0000 1.6e-001 -1.86 0.0 189 205 7726 8303 0.92195 1.7e-003 102 2 ATGAATR DREME-29 ATGAATR 6.3e-005 1.5e-006 -13.39 0.0 54 204 988 3201 0.26471 1.5e-008 101 2 CBCAG DREME-31 CTCAG 3.6e0000 8.8e-002 -2.43 0.0 180 206 21418 24328 0.87379 9.1e-004 102 2 GCATTMCA DREME-32 GCATTMCA 3.0e-006 7.2e-008 -16.45 0.0 115 203 510 755 0.56650 7.1e-010 101 2 AAAKGCAG DREME-33 AAAGGCAG 1.4e-004 3.4e-006 -12.59 0.0 65 203 601 1560 0.32020 3.4e-008 101 2 TATGTAA DREME-34 TATGTAA 6.9e-001 1.7e-002 -4.09 0.0 100 204 696 1287 0.49020 1.7e-004 101 2 CCACCTAS DREME-35 CCACCTAS 3.9e-002 9.5e-004 -6.96 0.0 77 203 247 522 0.37931 9.4e-006 101 2 CTACAGGY DREME-36 CTACAGGY 3.8e0000 9.2e-002 -2.39 0.0 95 203 244 450 0.46798 9.5e-004 101 2 CCACTAGA DREME-38 CCACTAGA 3.9e-002 9.5e-004 -6.96 0.0 149 203 265 316 0.73399 9.4e-006 101 ## # 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).