# 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 TGCCTGCRCCMCCYYB MEME-1 TGCCTGCRCCMCCYYB 3.8e-186 5.1e-189 -433.56 0.0 89 485 438 590 0.18351 2.1e-191 242 1 WAAAWAAATAAATAAATAAATAAATAAATAAATAAATAA MEME-2 WAAAWAAATAAATAAATAAATAAATAAATAAATAAATAA 2.6e-005 3.4e-008 -17.18 0.0 8 462 12 61 0.01732 1.5e-010 230 1 TGACTCATTCCRATTACCTGCT MEME-3 TGACTCATTCCRATTACCTGCT 2.5e-005 3.4e-008 -17.21 0.0 159 479 24 26 0.33194 1.4e-010 239 1 ACTCATTCCGATTACCTGCTCC MEME-4 ACTCATTCCGATTACCTGCTCC 5.9e-005 7.8e-008 -16.36 0.0 155 479 23 25 0.32359 3.3e-010 239 1 GAATGAGTCAGGGT MEME-7 GAATGAGTCAGGGT 3.6e0000 4.7e-003 -5.35 0.0 81 487 24 62 0.16632 2.0e-005 243 1 RGGSWGRRGGWGSAGG MEME-8 RGGSWGRRGGWGSAGG 2.1e-019 2.7e-022 -49.65 0.0 77 485 189 568 0.15876 1.1e-024 242 2 CCTGSRCC DREME-1 CCTGCACC 4.6e-062 6.1e-065 -147.85 0.0 91 493 199 317 0.18458 2.5e-067 246 2 CCTGGRTC DREME-2 CCTGGGTC 4.2e-013 5.6e-016 -35.13 0.0 119 493 64 97 0.24138 2.3e-018 246 2 GCWCCACC DREME-3 GCTCCACC 6.9e-015 9.2e-018 -39.23 0.0 127 493 87 137 0.25761 3.7e-020 246 2 MTGAGTCA DREME-4 ATGAGTCA 2.3e-003 3.0e-006 -12.70 0.0 131 493 40 67 0.26572 1.2e-008 246 2 AGGTRR DREME-5 AGGTRR 6.0e-008 8.0e-011 -23.25 0.0 117 495 180 465 0.23636 3.2e-013 247 2 GCCTGTR DREME-6 GCCTGTG 3.8e-004 5.0e-007 -14.50 0.0 78 494 63 190 0.15789 2.0e-009 246 2 CCSGCAC DREME-7 CCSGCAC 7.1e-011 9.4e-014 -29.99 0.0 54 494 54 148 0.10931 3.8e-016 246 3 M0609_1.02 DNMT1 NNCCGCNNNN 8.4e0000 1.1e-002 -4.49 0.0 211 491 229 438 0.42974 4.6e-005 245 3 M1963_1.02 (ZFY)_(Mus_musculus)_(DBD_0.97) SSSGSCBVGGCCTS 1.8e0000 2.3e-003 -6.05 0.0 443 487 534 557 0.90965 9.7e-006 243 3 M2277_1.02 FLI1 RCAGGAAGTGR 8.0e-001 1.1e-003 -6.84 0.0 262 490 362 577 0.53469 4.4e-006 244 3 M2321_1.02 TP63 NDRCAWGYHCARRCWTGYHY 1.7e0000 2.2e-003 -6.12 0.0 59 481 91 475 0.12266 9.2e-006 240 3 M4604_1.02 ZNF263 RRGGAGGASGVVGRGGRGGRG 2.8e0000 3.8e-003 -5.59 0.0 48 480 90 574 0.10000 1.6e-005 239 3 M4619_1.02 FOSL1 BGGTGASTCAK 9.7e-001 1.3e-003 -6.65 0.0 76 490 98 411 0.15510 5.3e-006 244 3 M5487_1.02 GCM2 BATGCGGGTR 1.2e-001 1.6e-004 -8.75 0.0 35 491 73 558 0.07128 6.5e-007 245 3 M5504_1.02 HES5 YGGCACGTGCCR 2.6e0000 3.4e-003 -5.68 0.0 85 489 68 236 0.17382 1.4e-005 244 3 M5506_1.02 HES7 YGGCACGTGCCR 1.2e0000 1.5e-003 -6.47 0.0 85 489 55 175 0.17382 6.4e-006 244 3 M5627_1.02 MESP1 NVCAGGTGYD 1.5e0000 2.0e-003 -6.24 0.0 61 491 111 591 0.12424 8.0e-006 245 3 M6322_1.02 KLF1 CAGGGTGKGGC 6.3e0000 8.4e-003 -4.78 0.0 158 490 233 581 0.32245 3.4e-005 244 3 M6547_1.02 ZFX SVGSSSSSCAGGCCBVGSC 7.7e-002 1.0e-004 -9.18 0.0 226 482 311 541 0.46888 4.3e-007 240 3 M6549_1.02 ZIC2 KGGGTGGTC 1.7e0000 2.2e-003 -6.10 0.0 38 492 77 598 0.07724 9.2e-006 245 ## # 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).