# 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 CATGTTCATGGATTGG MEME-1 CATGTTCATGGATTGG 2.3e-131 3.1e-134 -307.42 0.0 95 485 250 285 0.19588 1.3e-136 242 1 GTATRTSTKTSYATTT MEME-2 GTATRTSTKTSYATTT 2.2e-078 2.9e-081 -185.44 0.0 133 485 309 425 0.27423 1.2e-083 242 1 GTGTGTGTGTGTGTGTGTGTGT MEME-3 GTGTGTGTGTGTGTGTGTGTGT 7.2e-004 9.6e-007 -13.85 0.0 127 479 84 178 0.26514 4.0e-009 239 2 TTCATGRA DREME-1 TTCATGGA 3.6e-109 4.9e-112 -256.30 0.0 89 493 210 249 0.18053 2.0e-114 246 2 ATHCCATG DREME-2 ATMCCATG 6.7e-070 9.0e-073 -165.89 0.0 113 493 178 217 0.22921 3.7e-075 246 2 TCTTYCMA DREME-3 TCTTYCMA 5.4e-027 7.2e-030 -67.10 0.0 113 493 115 177 0.22921 2.9e-032 246 2 ARTATTG DREME-4 AATATTG 1.2e-028 1.6e-031 -70.90 0.0 110 494 113 173 0.22267 6.6e-034 246 2 AAAKAAAT DREME-5 AAAKAAAT 2.2e-010 2.9e-013 -28.87 0.0 191 493 133 199 0.38742 1.2e-015 246 2 CTACARA DREME-6 CTACARA 3.9e-009 5.3e-012 -25.97 0.0 268 494 159 199 0.54251 2.1e-014 246 2 CATYTTAA DREME-7 CATYTTAA 3.1e-017 4.2e-020 -44.61 0.0 133 493 72 97 0.26978 1.7e-022 246 2 GTCTTCY DREME-8 GTCTTCY 7.1e-019 9.5e-022 -48.40 0.0 100 494 88 151 0.20243 3.9e-024 246 3 M0108_1.02 (ARID5A)_(Mus_musculus)_(DBD_0.97) NDWAATATTKN 1.3e-002 1.8e-005 -10.95 0.0 112 490 150 440 0.22857 7.2e-008 244 3 M1583_1.02 (BBX)_(Mus_musculus)_(DBD_0.99) TTCATTGA 1.8e-047 2.4e-050 -114.23 0.0 89 493 189 346 0.18053 9.9e-053 246 3 M1889_1.02 MAX RRGCACATGK 2.4e-017 3.3e-020 -44.87 0.0 73 491 166 521 0.14868 1.3e-022 245 3 M5581_1.02 IRX2 CWTGTCRTGTWN 8.3e-001 1.1e-003 -6.80 0.0 109 489 164 533 0.22290 4.6e-006 244 3 M5582_1.02 IRX5 SWTGTYRTGTWN 1.5e0000 2.0e-003 -6.20 0.0 221 489 300 552 0.45194 8.3e-006 244 3 M5660_1.02 NFIA TTGGCANNDTGCCAR 3.7e-001 5.0e-004 -7.61 0.0 82 486 63 209 0.16872 2.0e-006 242 3 M5662_1.02 NFIB TTGGCAHNDTGCCAR 3.8e-001 5.2e-004 -7.57 0.0 82 486 65 218 0.16872 2.1e-006 242 3 M5835_1.02 SOX7 AACAATRWNCAKTGTT 3.7e-018 5.0e-021 -46.74 0.0 121 485 118 204 0.24948 2.1e-023 242 3 M5838_1.02 SOX8 AACAATRTGCAGTGTT 9.5e-010 1.3e-012 -27.39 0.0 111 485 70 126 0.22887 5.3e-015 242 3 M5972_1.02 ZNF410 GANTATTATGGGATGKM 3.3e-002 4.4e-005 -10.02 0.0 74 484 55 181 0.15289 1.8e-007 241 3 M6257_1.02 GATA5 WVANWGATAABTYRRHK 1.9e-003 2.6e-006 -12.86 0.0 214 484 288 507 0.44215 1.1e-008 241 3 M6269_1.02 HBP1 AYYCATTGA 1.3e-007 1.8e-010 -22.44 0.0 154 492 239 515 0.31301 7.4e-013 245 3 M6285_1.02 ONECUT1 WWTATTGATTTWDH 4.6e0000 6.2e-003 -5.08 0.0 13 487 28 445 0.02669 2.6e-005 243 3 M6291_1.02 HOXA1 CATCCATCMA 6.4e-018 8.6e-021 -46.20 0.0 87 491 189 528 0.17719 3.5e-023 245 3 M6293_1.02 HOXA7 KCCAATCKATYGAKB 8.8e-003 1.2e-005 -11.35 0.0 138 486 203 516 0.28395 4.9e-008 242 3 M6295_1.02 HOXB1 CCATCMATCW 1.1e-017 1.5e-020 -45.64 0.0 97 491 187 476 0.19756 6.2e-023 245 3 M6300_1.02 HOXC8 GSBHATYAATSAAR 3.8e-003 5.0e-006 -12.20 0.0 91 487 142 491 0.18686 2.1e-008 243 3 M6326_1.02 KLF8 CAGKGKGTG 4.0e-001 5.4e-004 -7.52 0.0 40 492 69 477 0.08130 2.2e-006 245 3 M6357_1.02 NANOG KTTAATGG 2.5e-007 3.3e-010 -21.83 0.0 87 493 157 518 0.17647 1.3e-012 246 3 M6361_1.02 NFATC1 AWGGAAWTTTCCD 6.2e0000 8.3e-003 -4.80 0.0 80 488 86 344 0.16393 3.4e-005 243 3 M6363_1.02 NFATC2 RWTTTTCCW 3.0e0000 4.0e-003 -5.51 0.0 60 492 98 526 0.12195 1.7e-005 245 3 M6364_1.02 NFATC3 RDTTTTCCA 3.3e-003 4.4e-006 -12.33 0.0 66 492 117 523 0.13415 1.8e-008 245 3 M6377_1.02 NKX2-8 TTCAAGKRC 1.0e-004 1.4e-007 -15.79 0.0 86 492 149 525 0.17480 5.7e-010 245 3 M6399_1.02 ONECUT2 DKSWTKWTATKGATTTTWYYT 2.5e-004 3.4e-007 -14.90 0.0 116 480 148 390 0.24167 1.4e-009 239 3 M6401_1.02 OTX2 HYYTAATCCBWKHDM 1.3e-001 1.7e-004 -8.69 0.0 56 486 90 466 0.11523 7.0e-007 242 3 M6410_1.02 PAX6 TSAWGCGTRAA 9.1e-006 1.2e-008 -18.22 0.0 42 490 94 537 0.08571 5.0e-011 244 3 M6412_1.02 PBX1 VHMATCAATCAAWTH 6.3e-003 8.5e-006 -11.68 0.0 102 486 166 536 0.20988 3.5e-008 242 3 M6473_1.02 SOX17 CAAMAATNHHCATTGTCS 1.2e-002 1.6e-005 -11.03 0.0 71 483 85 328 0.14700 6.7e-008 241 3 M6491_1.02 STAT5A YTTCYVRGAAWT 1.8e0000 2.4e-003 -6.02 0.0 281 489 302 448 0.57464 1.0e-005 244 3 M6492_1.02 STAT5B DTTTCYDGGAATT 1.4e0000 1.9e-003 -6.28 0.0 282 488 269 393 0.57787 7.7e-006 243 ## # 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).