# 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 RRRKGCTCWGYWAACA MEME-1 RRRKGCTCWGYWAACA 6.6e-164 8.8e-167 -382.36 0.0 109 485 421 531 0.22474 3.6e-169 242 1 TGGGAGGCYRAGGCGGGHGGATCACTTGAGS MEME-2 TGGGAGGCYRAGGCGGGHGGATCACTTGAGS 1.5e0000 2.0e-003 -6.22 0.0 68 470 28 83 0.14468 8.5e-006 234 1 GGCCAGGCTGGTCTCGAACTCC MEME-3 GGCCAGGCTGGTCTCGAACTCC 3.8e-002 5.0e-005 -9.89 0.0 145 479 39 63 0.30271 2.1e-007 239 1 GGAGGGGCRTCYRCCATTRCTGAGGCTTGAGTAGGYRGTTTTMCCCTCAC MEME-5 GGAGGGGCRTCYRCCATTRCTGAGGCTTGAGTAGGYRGTTTTMCCCTCAC 6.4e-002 8.5e-005 -9.37 0.0 71 451 8 8 0.15743 3.8e-007 225 1 CCWGCAYCTAGCACAGYGCCTGGCACAKAGC MEME-9 CCWGCAYCTAGCACAGYGCCTGGCACAKAGC 2.7e-002 3.5e-005 -10.25 0.0 108 470 26 43 0.22979 1.5e-007 234 1 AVTGTKTRCWGAGCAC MEME-10 AVTGTKTRCWGAGCAC 8.6e-090 1.1e-092 -211.70 0.0 115 485 312 445 0.23711 4.7e-095 242 2 GCTCWGY DREME-1 GCTCWGY 4.5e-017 6.0e-020 -44.26 0.0 80 494 129 337 0.16194 2.4e-022 246 2 GWTWACA DREME-2 GWTWACA 3.5e-012 4.7e-015 -32.99 0.0 104 494 114 253 0.21053 1.9e-017 246 2 GTGTTY DREME-3 GTGTTY 2.1e-013 2.8e-016 -35.83 0.0 97 495 136 335 0.19596 1.1e-018 247 2 GAGGCTB DREME-4 GAGGCTB 5.4e-024 7.2e-027 -60.19 0.0 80 494 128 288 0.16194 2.9e-029 246 3 M0428_1.02 (ZNF691)_(Mus_musculus)_(DBD_0.97) RKGAGYAC 3.8e-002 5.1e-005 -9.88 0.0 115 493 191 586 0.23327 2.1e-007 246 3 M0718_1.02 FOXK1 DNRTMAACAH 2.2e-006 2.9e-009 -19.67 0.0 91 491 174 579 0.18534 1.2e-011 245 3 M0719_1.02 FOXG1 RTAAACAW 7.6e-006 1.0e-008 -18.40 0.0 59 493 116 521 0.11968 4.1e-011 246 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 1.1e-002 1.4e-005 -11.16 0.0 53 489 104 564 0.10838 5.8e-008 244 3 M0736_1.02 (FOXK2)_(Mus_musculus)_(DBD_0.90) RTAAACAA 1.4e-005 1.9e-008 -17.77 0.0 31 493 80 579 0.06288 7.8e-011 246 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 1.6e-013 2.1e-016 -36.10 0.0 71 491 167 582 0.14460 8.6e-019 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 5.0e-004 6.6e-007 -14.22 0.0 29 491 72 581 0.05906 2.7e-009 245 3 M0756_1.02 (FOXN3)_(Strongylocentrotus_purpuratus)_(DBD_0.44) NNHMACANN 8.9e-012 1.2e-014 -32.06 0.0 44 492 111 531 0.08943 4.8e-017 245 3 M1581_1.02 (CIC)_(Mus_musculus)_(DBD_1.00) NNTGCTGACW 6.5e0000 8.7e-003 -4.75 0.0 39 491 74 574 0.07943 3.6e-005 245 3 M1863_1.02 FOXD1 GTAAACAW 4.1e-005 5.5e-008 -16.72 0.0 37 493 84 537 0.07505 2.2e-010 246 3 M2283_1.02 FOXP1 HWWADGTAAACAAAR 7.0e-001 9.4e-004 -6.97 0.0 86 486 141 554 0.17695 3.9e-006 242 3 M2385_1.02 FOXP2 RWGTAAACAVR 5.2e-006 6.9e-009 -18.79 0.0 28 490 73 546 0.05714 2.8e-011 244 3 M4567_1.02 FOXA2 NMWRWGTAAACANNN 1.8e-023 2.3e-026 -59.02 0.0 80 486 205 578 0.16461 9.6e-029 242 3 M4572_1.02 MAFF TGCTGACTCAGCAWW 1.1e0000 1.5e-003 -6.51 0.0 218 486 245 443 0.44856 6.2e-006 242 3 M5116_1.02 (ATOH8)_(Drosophila_melanogaster)_(DBD_0.70) RCCACCTGK 8.5e0000 1.1e-002 -4.48 0.0 44 492 81 577 0.08943 4.7e-005 245 3 M5430_1.02 FIGLA WMCACCTGKW 2.2e-001 2.9e-004 -8.14 0.0 61 491 112 580 0.12424 1.2e-006 245 3 M5446_1.02 FOXD4L2 RTAAACA 3.4e-009 4.6e-012 -26.11 0.0 32 494 90 580 0.06478 1.9e-014 246 3 M5460_1.02 FOXL1 RTAAACA 1.6e-007 2.2e-010 -22.25 0.0 60 494 129 565 0.12146 8.8e-013 246 3 M5517_1.02 HMBOX1 MYTAGTTAMS 2.8e0000 3.8e-003 -5.59 0.0 91 491 134 512 0.18534 1.5e-005 245 3 M5571_1.02 ID4 DVCAGGTGYN 4.4e0000 5.9e-003 -5.14 0.0 47 491 86 571 0.09572 2.4e-005 245 3 M5627_1.02 MESP1 NVCAGGTGYD 4.8e-005 6.4e-008 -16.56 0.0 61 491 127 583 0.12424 2.6e-010 245 3 M5636_1.02 MSC AACAGCTGTT 7.7e-001 1.0e-003 -6.88 0.0 207 491 250 476 0.42159 4.2e-006 245 3 M5965_1.02 ZIC4 DCDCMGCRGGGGGYC 6.3e-002 8.4e-005 -9.38 0.0 116 486 165 487 0.23868 3.5e-007 242 3 M5973_1.02 ZSCAN16 AGGTGTTCTGTTAACACT 4.5e-115 5.9e-118 -269.92 0.0 93 483 294 402 0.19255 2.5e-120 241 3 M6114_1.02 FOXA1 WAWGYAAAYA 7.6e-008 1.0e-010 -23.01 0.0 71 491 148 568 0.14460 4.2e-013 245 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 1.4e-001 1.9e-004 -8.58 0.0 64 488 116 566 0.13115 7.8e-007 243 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 4.6e-008 6.1e-011 -23.53 0.0 72 486 136 494 0.14815 2.5e-013 242 3 M6239_1.02 FOXF2 HWADGTAAACA 3.9e-011 5.3e-014 -30.58 0.0 70 490 152 549 0.14286 2.2e-016 244 3 M6241_1.02 FOXJ2 WAAAYAAAYA 3.0e-003 4.0e-006 -12.44 0.0 63 491 119 557 0.12831 1.6e-008 245 3 M6247_1.02 FOXO4 MRTAAACAA 8.6e-001 1.1e-003 -6.77 0.0 60 492 107 569 0.12195 4.7e-006 245 3 M6265_1.02 GLI2 GTGGGTGGTCY 3.8e0000 5.1e-003 -5.29 0.0 120 490 147 442 0.24490 2.1e-005 244 3 M6316_1.02 TCF4 VCAGGTGYD 1.3e-003 1.7e-006 -13.28 0.0 48 492 96 538 0.09756 6.9e-009 245 3 M6345_1.02 MITF VKCACATGWY 9.7e0000 1.3e-002 -4.35 0.0 117 491 175 564 0.23829 5.3e-005 245 3 M6516_1.02 TCF3 RRVCATCTGKT 4.2e-001 5.6e-004 -7.48 0.0 58 490 107 580 0.11837 2.3e-006 244 ## # 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).