# 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 CATAAGACAGACACTCCCAGAGCGGC MEME-1 CATAAGACAGACACTCCCAGAGCGGC 1.8e-037 2.4e-040 -91.21 0.0 117 475 69 69 0.24632 1.0e-042 237 1 AGGAGACCAGGGCDTATTT MEME-2 AGGAGACCAGGGCDTATTT 1.5e-027 2.0e-030 -68.40 0.0 144 482 67 69 0.29876 8.2e-033 240 1 TTTAKAGACCTCCCCC MEME-3 TTTAKAGACCTCCCCC 1.7e-024 2.3e-027 -61.35 0.0 137 485 68 75 0.28247 9.4e-030 242 1 GTTTCTGRTGAGAARTCWGCTG MEME-4 GTTTCTGRTGAGAARTCWGCTG 4.7e-016 6.2e-019 -41.93 0.0 53 479 56 126 0.11065 2.6e-021 239 1 GYVCAGCATGACTCAGCAGGTTTGGAGYGCAGGY MEME-5 GYVCAGCATGACTCAGCAGGTTTGGAGYGCAGGY 4.9e-011 6.5e-014 -30.36 0.0 49 467 19 22 0.10493 2.8e-016 233 1 TCCCTTATCTWCAACY MEME-6 TCCCTTATCTWCAACY 6.8e-024 9.0e-027 -59.97 0.0 101 485 44 45 0.20825 3.7e-029 242 1 MWWGBAAGCCWGARGRCAVTGS MEME-7 MWWGBAAGCCWGARGRCAVTGS 1.9e-030 2.6e-033 -75.05 0.0 181 479 163 202 0.37787 1.1e-035 239 1 GAGTGCACTCAGACCCAGYGGATTAACAT MEME-8 GAGTGCACTCAGACCCAGYGGATTAACAT 5.3e-018 7.0e-021 -46.40 0.0 66 472 28 29 0.13983 3.0e-023 235 1 TYAYRACTTACACAGACCATCTAYGACATGC MEME-9 TYAYRACTTACACAGACCATCTAYGACATGC 1.7e-005 2.2e-008 -17.61 0.0 200 470 27 27 0.42553 9.6e-011 234 1 AGAGAGAAACAAATATGCTCCAAATTTTGTT MEME-10 AGAGAGAAACAAATATGCTCCAAATTTTGTT 4.6e-005 6.0e-008 -16.62 0.0 86 470 13 13 0.18298 2.6e-010 234 2 AAGWCAGA DREME-1 AAGACAGA 2.0e-016 2.6e-019 -42.79 0.0 125 493 74 106 0.25355 1.1e-021 246 2 AGATAAGG DREME-2 AGATAAGG 3.6e-019 4.7e-022 -49.10 0.0 105 493 59 77 0.21298 1.9e-024 246 2 TCTGGSA DREME-3 TCTGGGA 2.4e-012 3.2e-015 -33.39 0.0 98 494 82 164 0.19838 1.3e-017 246 2 TCTMTAAA DREME-4 TCTMTAAA 6.0e-015 8.0e-018 -39.37 0.0 129 493 68 94 0.26166 3.2e-020 246 2 CWCCTGCA DREME-5 CTCCTGCA 8.0e-009 1.1e-011 -25.28 0.0 157 493 97 158 0.31846 4.3e-014 246 2 MTGAAATA DREME-6 ATGAAATA 3.5e-010 4.7e-013 -28.39 0.0 91 493 55 103 0.18458 1.9e-015 246 2 RTGACTCA DREME-8 ATGACTCA 5.3e-002 7.0e-005 -9.57 0.0 151 493 78 155 0.30629 2.8e-007 246 2 CAACYGCA DREME-9 CAACTGCA 2.4e-008 3.2e-011 -24.17 0.0 57 493 53 156 0.11562 1.3e-013 246 2 ATGCATTC DREME-10 ATGCATTC 4.4e-002 5.8e-005 -9.76 0.0 169 493 109 211 0.34280 2.3e-007 246 2 ACAGCWGA DREME-13 ACAGCWGA 1.6e0000 2.1e-003 -6.18 0.0 109 493 61 164 0.22110 8.5e-006 246 3 M0216_1.02 (NHLH2)_(Mus_musculus)_(DBD_1.00) NGCAGCTGYN 2.5e-003 3.2e-006 -12.64 0.0 21 491 55 557 0.04277 1.3e-008 245 3 M0398_1.02 (ZSCAN10)_(Mus_musculus)_(DBD_0.82) NGKRAGTGCNN 6.4e-007 8.5e-010 -20.89 0.0 92 490 168 540 0.18776 3.5e-012 244 3 M0424_1.02 (SNAI3)_(Mus_musculus)_(DBD_0.75) NNTGACAKNN 1.2e-001 1.6e-004 -8.72 0.0 377 491 503 592 0.76782 6.7e-007 245 3 M0428_1.02 (ZNF691)_(Mus_musculus)_(DBD_0.97) RKGAGYAC 4.8e0000 6.4e-003 -5.06 0.0 87 493 139 567 0.17647 2.6e-005 246 3 M0442_1.02 (ZBTB3)_(Mus_musculus)_(DBD_1.00) NNTGCAGYG 6.9e-004 9.1e-007 -13.91 0.0 128 492 220 596 0.26016 3.7e-009 245 3 M0603_1.02 CGBP NNNBCGK 7.4e0000 9.8e-003 -4.63 0.0 68 494 75 344 0.13765 4.0e-005 246 3 M0609_1.02 DNMT1 NNCCGMNNNN 9.3e-001 1.2e-003 -6.70 0.0 69 491 86 380 0.14053 5.0e-006 245 3 M1432_1.02 NR2E1 NYTGACCTCD 6.7e0000 8.9e-003 -4.73 0.0 135 491 193 545 0.27495 3.6e-005 245 3 M1581_1.02 (CIC)_(Mus_musculus)_(DBD_1.00) NNTGCTGACW 8.3e-006 1.1e-008 -18.32 0.0 279 491 406 580 0.56823 4.5e-011 245 3 M1926_1.02 ZEB1 CAGGTGWGB 1.7e0000 2.2e-003 -6.11 0.0 54 492 91 528 0.10976 9.1e-006 245 3 M1928_1.02 NFKB1 KGGRMTTTCCM 9.4e0000 1.2e-002 -4.39 0.0 206 490 265 523 0.42041 5.1e-005 244 3 M1934_1.02 ESR1 RGGTCAGGGTGACCTKGVNN 4.2e0000 5.5e-003 -5.21 0.0 9 481 24 486 0.01871 2.3e-005 240 3 M2264_1.02 (ATOH1)_(Mus_musculus)_(DBD_1.00) RCCAKCTG 5.1e-003 6.8e-006 -11.90 0.0 115 493 187 557 0.23327 2.8e-008 246 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 5.2e0000 6.9e-003 -4.98 0.0 54 488 87 508 0.11066 2.9e-005 243 3 M2321_1.02 TP63 NDRCAWGYHCARRCWTGYHY 4.4e0000 5.8e-003 -5.16 0.0 21 481 43 499 0.04366 2.4e-005 240 3 M4344_1.02 (ARID2)_(Saccharomyces_cerevisiae)_(DBD_0.26) SGTTGCYA 5.8e-003 7.7e-006 -11.78 0.0 175 493 262 560 0.35497 3.1e-008 246 3 M4471_1.02 PAX5 BCAGYSRAGCGTGAC 8.2e-001 1.1e-003 -6.83 0.0 140 486 195 513 0.28807 4.5e-006 242 3 M4479_1.02 TCF12 VSAGCAGSTGB 1.9e0000 2.5e-003 -5.98 0.0 56 490 94 528 0.11429 1.0e-005 244 3 M4612_1.02 CTCFL CCRSCAGGGGGCGCY 1.1e-001 1.4e-004 -8.84 0.0 194 486 188 356 0.39918 6.0e-007 242 3 M5292_1.02 ATF4 RKATGAYGCAATM 8.4e-004 1.1e-006 -13.72 0.0 88 488 112 367 0.18033 4.5e-009 243 3 M5621_1.02 MEIS3 SCTGTCAH 2.0e-001 2.7e-004 -8.22 0.0 369 493 485 583 0.74848 1.1e-006 246 3 M5664_1.02 NFIX TTGGCANNNHGCCAR 3.1e0000 4.2e-003 -5.48 0.0 24 486 41 411 0.04938 1.7e-005 242 3 M5689_1.02 NRL DWWNTGCTGAC 2.3e0000 3.0e-003 -5.79 0.0 290 490 400 591 0.59184 1.2e-005 244 3 M5857_1.02 SPDEF AMCCGGATGTW 9.0e0000 1.2e-002 -4.43 0.0 308 490 267 367 0.62857 4.9e-005 244 3 M5955_1.02 YY2 WAATGGCGGWY 4.7e0000 6.3e-003 -5.07 0.0 74 490 111 505 0.15102 2.6e-005 244 3 M6265_1.02 GLI2 GTGGGTGGTCY 2.5e-003 3.4e-006 -12.60 0.0 196 490 202 370 0.40000 1.4e-008 244 3 M6271_1.02 HES1 KGKCKCGTGBCKB 9.6e0000 1.3e-002 -4.36 0.0 174 488 234 533 0.35656 5.3e-005 243 3 M6278_1.02 HLTF KANKGCTGSMAM 3.8e0000 5.0e-003 -5.31 0.0 211 489 305 591 0.43149 2.0e-005 244 3 M6289_1.02 HOXA9 WCATAAAYYRTH 2.2e0000 2.9e-003 -5.86 0.0 75 489 117 523 0.15337 1.2e-005 244 3 M6316_1.02 TCF4 VCAGGTGYD 5.3e-001 7.0e-004 -7.27 0.0 14 492 34 492 0.02846 2.8e-006 245 3 M6330_1.02 MAFA BTGCTGACBMYGCARYHTYCV 2.5e0000 3.4e-003 -5.70 0.0 230 480 311 546 0.47917 1.4e-005 239 3 M6331_1.02 MAFB WGCTGACDS 9.7e-002 1.3e-004 -8.96 0.0 62 492 117 589 0.12602 5.2e-007 245 3 M6332_1.02 MAF KTGCTGAC 4.9e-005 6.5e-008 -16.55 0.0 255 493 383 595 0.51724 2.6e-010 246 3 M6333_1.02 MAFG MATGACT 5.3e0000 7.1e-003 -4.95 0.0 64 494 107 561 0.12955 2.9e-005 246 3 M6339_1.02 MECP2 YYCCGGS 6.5e-003 8.5e-006 -11.67 0.0 66 494 113 508 0.13360 3.5e-008 246 3 M6343_1.02 MEIS1 CDTWAAVCTGTCA 1.0e-002 1.3e-005 -11.22 0.0 68 488 118 518 0.13934 5.5e-008 243 3 M6353_1.02 MYF6 GCAGSTG 5.2e-004 6.8e-007 -14.20 0.0 58 494 108 518 0.11741 2.8e-009 246 3 M6354_1.02 MYOD1 RACAGSTGS 9.9e0000 1.3e-002 -4.34 0.0 74 492 119 559 0.15041 5.4e-005 245 3 M6355_1.02 MYOG YRACAGCTGCWGC 1.4e-001 1.9e-004 -8.56 0.0 56 488 94 492 0.11475 7.9e-007 243 3 M6361_1.02 NFATC1 AWGGAAWTTTCCD 7.8e-001 1.0e-003 -6.88 0.0 424 488 419 448 0.86885 4.2e-006 243 3 M6401_1.02 OTX2 HYYTAATCCBWKHDM 6.1e0000 8.1e-003 -4.82 0.0 46 486 76 499 0.09465 3.3e-005 242 3 M6429_1.02 POU6F1 CATAAWTTATGCR 3.0e0000 3.9e-003 -5.55 0.0 114 488 98 286 0.23361 1.6e-005 243 3 M6449_1.02 REL DKGGRNWTTCCV 7.7e0000 1.0e-002 -4.59 0.0 221 489 303 566 0.45194 4.2e-005 244 3 M6464_1.02 SMAD2 GTGTCHGKCTV 1.0e-004 1.3e-007 -15.84 0.0 32 490 79 576 0.06531 5.4e-010 244 3 M6465_1.02 SMAD3 STGTCTGBCY 5.3e-001 7.0e-004 -7.26 0.0 97 491 163 589 0.19756 2.9e-006 245 3 M6466_1.02 SMAD4 TGTCTGBCY 1.8e0000 2.4e-003 -6.03 0.0 84 492 142 590 0.17073 9.8e-006 245 3 M6516_1.02 TCF3 RRVCATCTGKT 1.3e-003 1.7e-006 -13.28 0.0 44 490 95 572 0.08980 7.0e-009 244 ## # 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).