# 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 VRGRCTTTTATTTTGAARNV MEME-1 VRGRCTTTTATTTTGAARNV 2.7e-144 3.7e-147 -337.18 0.0 95 481 355 470 0.19751 1.5e-149 240 1 SSGTYDCCATRGCAACVGSSB MEME-2 SSGTYDCCATRGCAACVGSSB 5.7e-045 7.6e-048 -108.49 0.0 88 480 177 317 0.18333 3.2e-050 239 1 YBGKYTCCMTGGCRAC MEME-4 YBGKYTCCMTGGCRAC 3.5e-037 4.7e-040 -90.56 0.0 85 485 170 340 0.17526 1.9e-042 242 1 RRGGACTYTTA MEME-8 RRGGACTYTTA 2.3e-055 3.0e-058 -132.44 0.0 84 490 174 287 0.17143 1.2e-060 244 2 RCTYTTA DREME-1 RCTYTTA 5.2e-074 6.9e-077 -175.37 0.0 86 494 215 338 0.17409 2.8e-079 246 2 GTTGCYA DREME-2 GTTGCYA 1.2e-037 1.6e-040 -91.66 0.0 92 494 118 182 0.18623 6.4e-043 246 2 GTYWCCA DREME-3 GTYWCCA 2.0e-014 2.7e-017 -38.14 0.0 84 494 90 202 0.17004 1.1e-019 246 2 CAWAATA DREME-4 CAAAATA 1.3e-031 1.7e-034 -77.77 0.0 102 494 107 159 0.20648 6.8e-037 246 2 GGCRAC DREME-5 GGCRAC 5.4e-032 7.2e-035 -78.62 0.0 91 495 144 274 0.18384 2.9e-037 247 3 M0104_1.02 (ARID3B)_(Mus_musculus)_(DBD_0.99) AWATTAATWAN 6.1e0000 8.1e-003 -4.81 0.0 42 490 67 471 0.08571 3.3e-005 244 3 M0105_1.02 (ARID3C)_(Mus_musculus)_(DBD_0.87) NTTTDATHN 4.2e0000 5.6e-003 -5.18 0.0 26 492 52 535 0.05285 2.3e-005 245 3 M0594_1.02 (LIN54)_(Gallus_gallus)_(DBD_0.98) DTTTRAATH 9.5e0000 1.3e-002 -4.36 0.0 100 492 135 484 0.20325 5.2e-005 245 3 M0897_1.02 HOXB13 DTTWAYDRBN 1.2e0000 1.6e-003 -6.44 0.0 19 491 43 532 0.03870 6.5e-006 245 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 8.5e-005 1.1e-007 -15.99 0.0 39 491 86 536 0.07943 4.7e-010 245 3 M1528_1.02 (RFX6)_(Mus_musculus)_(DBD_0.66) VCNTRGYWAC 2.6e-023 3.5e-026 -58.62 0.0 77 491 202 589 0.15682 1.4e-028 245 3 M1529_1.02 (RFX7)_(Mus_musculus)_(DBD_1.00) VCNTRGCAAC 3.7e-023 4.9e-026 -58.27 0.0 79 491 205 590 0.16090 2.0e-028 245 3 M1582_1.02 (HMG20B)_(Mus_musculus)_(DBD_0.94) NWAWATAATWN 2.6e-003 3.5e-006 -12.57 0.0 26 490 55 453 0.05306 1.4e-008 244 3 M1925_1.02 CEBPA DRTTRTGCAAT 8.1e-004 1.1e-006 -13.74 0.0 20 490 52 519 0.04082 4.4e-009 244 3 M2319_1.02 TCF7L2 TBYCTTTGAWSTYN 1.5e0000 1.9e-003 -6.24 0.0 35 487 68 545 0.07187 8.0e-006 243 3 M2392_1.02 RFX2 GTYDCCATGGCAACVRVNN 1.8e-027 2.4e-030 -68.20 0.0 58 482 159 486 0.12033 1.0e-032 240 3 M4344_1.02 (ARID2)_(Saccharomyces_cerevisiae)_(DBD_0.26) SGTTGCYA 3.8e-024 5.0e-027 -60.56 0.0 89 493 218 573 0.18053 2.0e-029 246 3 M4467_1.02 MEF2C NDKCYAAAAATAGMH 2.8e-001 3.7e-004 -7.89 0.0 16 486 39 510 0.03292 1.5e-006 242 3 M4476_1.02 RFX5 TCABYWGTTGCYRGG 1.3e-014 1.8e-017 -38.56 0.0 92 486 199 564 0.18930 7.4e-020 242 3 M5322_1.02 CPEB1 YTTTTATY 1.3e-011 1.8e-014 -31.68 0.0 47 493 118 548 0.09533 7.1e-017 246 3 M5544_1.02 HOXC10 DTTTWATKDB 1.2e-001 1.5e-004 -8.77 0.0 25 491 55 529 0.05092 6.3e-007 245 3 M5551_1.02 HOXC12 TTTTATTRC 9.4e-005 1.3e-007 -15.89 0.0 38 492 83 525 0.07724 5.1e-010 245 3 M5553_1.02 HOXC13 CYAATAAAAH 4.0e-002 5.4e-005 -9.84 0.0 39 491 75 510 0.07943 2.2e-007 245 3 M5557_1.02 HOXD12 GTAATAAAA 4.4e-001 5.9e-004 -7.44 0.0 38 492 72 524 0.07724 2.4e-006 245 3 M5621_1.02 MEIS3 SCTGTCAH 3.6e-002 4.8e-005 -9.93 0.0 21 493 54 591 0.04260 2.0e-007 246 3 M5777_1.02 RFX4 NGTWRCCATGGYWACS 6.9e-029 9.2e-032 -71.46 0.0 61 485 149 414 0.12577 3.8e-034 242 3 M5804_1.02 SCRT1 RWGCAACAGGTGKBH 6.0e0000 8.0e-003 -4.82 0.0 88 486 103 389 0.18107 3.3e-005 242 3 M6173_1.02 CEBPG VAGATTGCAHAAT 4.9e0000 6.5e-003 -5.04 0.0 28 488 54 522 0.05738 2.7e-005 243 3 M6236_1.02 FOXC2 YCTRDSWAAACAAAC 8.9e0000 1.2e-002 -4.44 0.0 74 486 97 430 0.15226 4.9e-005 242 3 M6274_1.02 HIC1 GGGKTGCCC 1.5e-008 2.0e-011 -24.62 0.0 32 492 86 550 0.06504 8.3e-014 245 3 M6279_1.02 HMGA1 AAAATWN 1.8e-004 2.4e-007 -15.26 0.0 22 494 58 541 0.04453 9.6e-010 246 3 M6290_1.02 HOXA13 CCAATAAWAHC 4.1e-001 5.5e-004 -7.51 0.0 66 490 109 520 0.13469 2.2e-006 244 3 M6301_1.02 HOXD10 AATTAAARCA 1.4e-002 1.9e-005 -10.89 0.0 21 491 52 541 0.04277 7.6e-008 245 3 M6308_1.02 IRF2 SGAAAGYGAAASYV 4.9e0000 6.5e-003 -5.03 0.0 27 487 54 540 0.05544 2.7e-005 243 3 M6342_1.02 MEF2D BCTAWAAATAGC 7.2e0000 9.7e-003 -4.64 0.0 23 489 42 464 0.04703 4.0e-005 244 3 M6350_1.02 MYB CMGTTRD 5.9e0000 7.8e-003 -4.85 0.0 58 494 98 559 0.11741 3.2e-005 246 3 M6451_1.02 RFX1 GTTGCYAGGSRA 5.4e-019 7.2e-022 -48.68 0.0 83 489 193 552 0.16973 3.0e-024 244 3 M6453_1.02 RFX3 TYRCCATGGYAACV 2.7e-031 3.6e-034 -77.00 0.0 107 487 219 445 0.21971 1.5e-036 243 3 M6475_1.02 SOX2 WTTTGCATRACAAWGG 9.3e-005 1.2e-007 -15.90 0.0 25 485 64 533 0.05155 5.1e-010 242 3 M6486_1.02 SPZ1 CGGCKGWWACMBYGGG 1.8e0000 2.3e-003 -6.05 0.0 67 485 107 512 0.13814 9.7e-006 242 3 M6545_1.02 HIVEP2 GGYDGGGWAACYSS 2.4e0000 3.2e-003 -5.73 0.0 55 487 100 579 0.11294 1.3e-005 243 3 M6555_1.02 ZNF333 SKATAATGA 7.6e0000 1.0e-002 -4.59 0.0 24 492 43 451 0.04878 4.1e-005 245 3 M6559_1.02 ZNF589 CCMASGGKWWYWRCCS 5.3e0000 7.0e-003 -4.96 0.0 287 485 383 567 0.59175 2.9e-005 242 ## # 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).