# 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 KGTGGGCCCCRS MEME-1 KGTGGGCCCCRS 1.5e-173 2.0e-176 -404.58 0.0 71 489 358 506 0.14519 8.0e-179 244 1 YKGCCCCTTTAAGR MEME-2 YKGCCCCTTTAAGR 7.8e-020 1.1e-022 -50.61 0.0 143 487 197 353 0.29363 4.3e-025 243 1 WATSAAGTKAARATGAKGTCAY MEME-4 WATSAAGTKAARATGAKGTCAY 2.7e-001 3.7e-004 -7.91 0.0 85 479 19 34 0.17745 1.5e-006 239 1 TSTGGNCCYRTTTGGWKCTTAANTRAAWKRHAHCGABTGTAGW MEME-6 TSTGGNCCYRTTTGGWKCTTAANTRAAWKRHAHCGABTGTAGW 1.7e0000 2.3e-003 -6.06 0.0 46 458 5 5 0.10044 1.0e-005 228 1 RCTGCCMCCTVGTGGC MEME-10 RCTGCCMCCTVGTGGC 9.7e0000 1.3e-002 -4.34 0.0 81 485 24 64 0.16701 5.4e-005 242 2 GGNCCCAC DREME-1 GGSCCCAC 1.1e-165 1.4e-168 -386.48 0.0 75 493 307 391 0.15213 5.8e-171 246 2 TTTAARR DREME-2 TTTAAGR 1.5e-007 2.0e-010 -22.32 0.0 198 494 154 246 0.40081 8.2e-013 246 2 GGAAATD DREME-3 GGAAATG 6.0e0000 8.0e-003 -4.82 0.0 112 494 52 135 0.22672 3.3e-005 246 3 M0404_1.02 (ZNF202)_(Mus_musculus)_(DBD_0.87) NNNKGGGGSV 1.6e0000 2.1e-003 -6.14 0.0 61 491 111 595 0.12424 8.8e-006 245 3 M0422_1.02 (ZIC5)_(Mus_musculus)_(DBD_0.99) SYRGGGGGTM 9.2e-002 1.2e-004 -9.00 0.0 35 491 77 599 0.07128 5.1e-007 245 3 M5116_1.02 (ATOH8)_(Drosophila_melanogaster)_(DBD_0.70) RCCACCTGK 1.4e-001 1.9e-004 -8.56 0.0 60 492 110 572 0.12195 7.8e-007 245 3 M5293_1.02 ATF7 BKATGACGTCATHN 2.8e-001 3.7e-004 -7.89 0.0 207 487 139 241 0.42505 1.5e-006 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.6e-001 2.1e-004 -8.46 0.0 245 487 97 137 0.50308 8.7e-007 243 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 1.6e0000 2.1e-003 -6.16 0.0 207 487 145 259 0.42505 8.7e-006 243 3 M5491_1.02 GLIS2 CDYYGCGGGGGGTC 1.9e-001 2.5e-004 -8.28 0.0 77 487 105 422 0.15811 1.0e-006 243 3 M5627_1.02 MESP1 NVCAGGTGYD 5.7e0000 7.7e-003 -4.87 0.0 71 491 122 592 0.14460 3.2e-005 245 3 M5962_1.02 ZBTB7C NTCGGTGGTCGY 6.1e-004 8.2e-007 -14.02 0.0 43 489 95 579 0.08793 3.3e-009 244 3 M5965_1.02 ZIC4 DCDCMGCGGGGGGYC 5.2e0000 6.9e-003 -4.97 0.0 98 486 149 543 0.20165 2.9e-005 242 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 2.3e0000 3.1e-003 -5.79 0.0 207 489 158 288 0.42331 1.3e-005 244 3 M6144_1.02 TFAP2B BCCCBCRGGC 2.1e0000 2.8e-003 -5.88 0.0 115 491 182 584 0.23422 1.1e-005 245 3 M6152_1.02 ATF1 VTGACGTCAV 5.6e-001 7.5e-004 -7.20 0.0 273 491 296 447 0.55601 3.1e-006 245 3 M6267_1.02 GLIS3 GYGGGGGGTM 3.1e0000 4.2e-003 -5.47 0.0 57 491 102 582 0.11609 1.7e-005 245 3 M6306_1.02 INSM1 TGTMAGGGGGCR 5.2e-002 6.9e-005 -9.58 0.0 273 489 326 487 0.55828 2.8e-007 244 3 M6322_1.02 KLF1 CAGGGTGKGGC 6.5e-003 8.7e-006 -11.65 0.0 46 490 96 574 0.09388 3.6e-008 244 3 M6346_1.02 MLXIPL VCACGVSGKKGBCMCRTGC 8.5e0000 1.1e-002 -4.48 0.0 46 482 60 373 0.09544 4.8e-005 240 3 M6352_1.02 MYCN CCACGTGS 8.5e0000 1.1e-002 -4.48 0.0 81 493 117 505 0.16430 4.6e-005 246 3 M6422_1.02 PLAGL1 CRGGGGGCCC 9.8e-053 1.3e-055 -126.37 0.0 59 491 221 578 0.12016 5.4e-058 245 3 M6527_1.02 TWIST1 MCCCAGGTGK 1.9e-002 2.6e-005 -10.57 0.0 63 491 108 512 0.12831 1.0e-007 245 ## # 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).