# 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 WGGGTGTGGYYS MEME-1 WGGGTGTGGYYS 1.5e-067 2.6e-070 -160.24 0.0 99 489 344 663 0.20245 1.1e-072 244 1 VWGATAAR MEME-2 VWGATAAR 1.3e-040 2.1e-043 -98.26 0.0 183 493 345 504 0.37120 8.6e-046 246 2 MCRCCCW DREME-1 MCACCCW 7.0e-059 1.2e-061 -140.31 0.0 126 494 343 587 0.25506 4.7e-064 246 2 TTATCW DREME-2 TTATCW 7.3e-040 1.2e-042 -96.51 0.0 175 495 330 496 0.35354 4.9e-045 247 3 MA0006.1 Arnt::Ahr YGCGTG 4.1e0000 6.9e-003 -4.97 0.0 149 495 227 600 0.30101 2.8e-005 247 3 MA0027.1 En1 DAGTDGTDBYC 5.6e-002 9.4e-005 -9.27 0.0 130 490 293 854 0.26531 3.9e-007 244 3 MA0029.1 Mecom AAGAYAAGATAANA 7.6e-001 1.3e-003 -6.67 0.0 179 487 89 165 0.36756 5.2e-006 243 3 MA0048.1 NHLH1 NCGCAGCTGCGB 7.0e0000 1.2e-002 -4.45 0.0 89 489 112 433 0.18200 4.8e-005 244 3 MA0121.1 ARR10 AGATHYKV 7.5e-001 1.2e-003 -6.69 0.0 139 493 247 684 0.28195 5.1e-006 246 3 MA0039.2 Klf4 DGGGYGKGGC 1.9e-062 3.2e-065 -148.51 0.0 111 491 369 697 0.22607 1.3e-067 245 3 MA0002.2 RUNX1 BBYTGTGGTTT 3.7e-001 6.2e-004 -7.39 0.0 128 490 267 798 0.26122 2.5e-006 244 3 MA0199.1 Optix TGATA 2.9e-011 4.9e-014 -30.64 0.0 156 496 248 506 0.31452 2.0e-016 247 3 MA0204.1 Six4 TGAYAC 2.0e-002 3.4e-005 -10.29 0.0 155 495 270 662 0.31313 1.4e-007 247 3 MA0207.1 achi TGACAG 5.2e0000 8.6e-003 -4.75 0.0 151 495 202 522 0.30505 3.5e-005 247 3 MA0227.1 hth TGACAK 6.2e0000 1.0e-002 -4.56 0.0 117 495 129 397 0.23636 4.2e-005 247 3 MA0259.1 HIF1A::ARNT VBACGTGC 6.0e0000 1.0e-002 -4.60 0.0 111 493 122 390 0.22515 4.1e-005 246 3 MA0270.1 AFT2 SACACCCB 1.3e-030 2.2e-033 -75.22 0.0 129 493 246 457 0.26166 8.8e-036 246 3 MA0289.1 DAL80 CGATAAG 3.0e-032 5.0e-035 -78.98 0.0 138 494 308 578 0.27935 2.0e-037 246 3 MA0298.1 FZF1 CTATCA 5.2e-002 8.7e-005 -9.35 0.0 183 495 378 831 0.36970 3.5e-007 247 3 MA0300.1 GAT1 YYGATAAG 3.1e-035 5.3e-038 -85.84 0.0 183 493 348 529 0.37120 2.1e-040 246 3 MA0307.1 GLN3 GATAA 9.5e-030 1.6e-032 -73.22 0.0 186 496 473 801 0.37500 6.4e-035 247 3 MA0309.1 GZF3 YGATAASR 1.4e-032 2.3e-035 -79.76 0.0 151 493 322 567 0.30629 9.4e-038 246 3 MA0333.1 MET31 RNTGTGGCG 4.8e-003 8.1e-006 -11.72 0.0 48 492 78 422 0.09756 3.3e-008 245 3 MA0334.1 MET32 MGCCACA 9.7e-006 1.6e-008 -17.93 0.0 114 494 264 795 0.23077 6.6e-011 246 3 MA0403.1 TBF1 ARCCCTAV 6.6e0000 1.1e-002 -4.50 0.0 177 493 343 804 0.35903 4.5e-005 246 3 MA0425.1 YGR067C VCCCCDCNNNNNNN 1.2e-002 2.0e-005 -10.82 0.0 109 487 165 506 0.22382 8.2e-008 243 3 MA0431.1 YML081W NCCCCDCWH 5.3e0000 8.8e-003 -4.73 0.0 84 492 119 489 0.17073 3.6e-005 245 3 MA0443.1 btd RRGGGGCGKR 4.6e-006 7.8e-009 -18.67 0.0 95 491 144 442 0.19348 3.2e-011 245 3 MA0450.1 hkb KGGGCGTGA 2.5e-015 4.1e-018 -40.03 0.0 96 492 127 292 0.19512 1.7e-020 245 3 MA0145.2 Tcfcp2l1 CCAGYYYVADCCRG 4.9e0000 8.3e-003 -4.80 0.0 105 487 178 625 0.21561 3.4e-005 243 3 MA0472.1 EGR2 SHYMCRCCCACRCMC 1.2e-001 1.9e-004 -8.54 0.0 56 486 93 487 0.11523 8.1e-007 242 3 MA0482.1 Gata4 YCTTATCTSHB 9.3e-030 1.6e-032 -73.24 0.0 196 490 344 513 0.40000 6.4e-035 244 3 MA0493.1 Klf1 RRCCACACCCW 3.6e-078 6.0e-081 -184.72 0.0 100 490 356 647 0.20408 2.4e-083 244 3 MA0499.1 Myod1 NSCAGCTGYYNYB 2.5e0000 4.1e-003 -5.50 0.0 300 488 266 370 0.61475 1.7e-005 243 3 MA0500.1 Myog RRCAGCTGSNV 7.0e-001 1.2e-003 -6.75 0.0 102 490 98 307 0.20816 4.8e-006 244 3 MA0513.1 SMAD2::SMAD3::SMAD4 CTGTCTGDCACCT 1.2e0000 2.1e-003 -6.18 0.0 170 488 241 549 0.34836 8.6e-006 243 3 MA0516.1 SP2 GYCCCGCCYCYBSSS 5.9e-003 9.8e-006 -11.53 0.0 130 486 222 603 0.26749 4.1e-008 242 3 MA0521.1 Tcf12 RACAGCTGSNV 1.4e-001 2.4e-004 -8.33 0.0 102 490 109 341 0.20816 9.9e-007 244 3 MA0522.1 Tcf3 SMCAGCTGCHB 9.7e-001 1.6e-003 -6.43 0.0 96 490 117 408 0.19592 6.6e-006 244 3 MA0525.1 TP63 DDRCAWGYYCARRCWTGYHY 7.8e0000 1.3e-002 -4.34 0.0 55 481 68 369 0.11435 5.4e-005 240 3 MA0007.2 AR ARGAACABWVTGTNC 3.4e0000 5.7e-003 -5.18 0.0 66 486 101 498 0.13580 2.3e-005 242 3 MA0035.3 Gata1 TYCTTATCTSY 7.9e-039 1.3e-041 -94.13 0.0 184 490 320 459 0.37551 5.4e-044 244 3 MA0036.2 GATA2 WRDTTCTTATCTSH 1.9e-043 3.2e-046 -104.75 0.0 179 487 339 488 0.36756 1.3e-048 243 3 MA0037.2 GATA3 AGATAAGA 5.8e-016 9.6e-019 -41.48 0.0 177 493 151 225 0.35903 3.9e-021 246 3 MA0100.2 Myb BHAACTGYCA 4.2e0000 7.0e-003 -4.96 0.0 67 491 82 386 0.13646 2.9e-005 245 3 MA0079.3 SP1 GCCCCKCCCCC 3.4e-006 5.7e-009 -18.98 0.0 112 490 198 561 0.22857 2.4e-011 244 3 MA0140.2 TAL1::GATA1 MTTATCWSNNNNNHVCAG 5.6e-033 9.4e-036 -80.66 0.0 145 483 251 413 0.30021 3.9e-038 241 3 MA0531.1 CTCF CCRMYAGRTGGCGCY 3.5e-002 5.9e-005 -9.74 0.0 162 486 180 394 0.33333 2.4e-007 242 3 MA0542.1 ELT-3 TCTTATCA 8.3e-013 1.4e-015 -34.21 0.0 95 493 70 132 0.19270 5.6e-018 246 3 MA0545.1 HLH-1 SAACAGCTGNC 6.7e-003 1.1e-005 -11.40 0.0 100 490 125 390 0.20408 4.6e-008 244 3 MA0575.1 AtMYB77 NADYGACRGTTAS 3.1e-001 5.2e-004 -7.56 0.0 148 488 131 305 0.30328 2.1e-006 243 3 MA0599.1 KLF5 GCCCCDCCCH 3.6e-043 6.0e-046 -104.12 0.0 105 491 308 653 0.21385 2.5e-048 245 ## # 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).