# 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 AYAMAYAMAYAMAYAMAYAMAYAMAYAM MEME-1 AYAMAYAMAYAMAYAMAYAMAYAMAYAM 1.3e-032 1.8e-035 -80.03 0.0 41 473 104 287 0.08668 7.5e-038 236 1 CYYTCYYTCTYTCTCTCYCTCY MEME-2 CYYTCYYTCTYTCTCTCYCTCY 5.5e0000 7.4e-003 -4.91 0.0 57 479 58 287 0.11900 3.1e-005 239 1 CACACACACACACACACACMMM MEME-3 CACACACACACACACACACMMM 1.7e-009 2.2e-012 -26.84 0.0 137 479 166 344 0.28601 9.3e-015 239 1 TTGAGACRGAGTCTYRCTCTGT MEME-5 TTGAGACRGAGTCTYRCTCTGT 2.9e-003 3.9e-006 -12.46 0.0 89 479 55 141 0.18580 1.6e-008 239 1 TTATTTATTTATTTAT MEME-6 TTATTTATTTATTTAT 1.9e-025 2.5e-028 -63.54 0.0 45 485 77 190 0.09278 1.0e-030 242 1 KGTKGTGWKKGTGDKG MEME-7 KGTKGTGWKKGTGDKG 2.0e-002 2.6e-005 -10.55 0.0 89 485 121 421 0.18351 1.1e-007 242 1 CACACACAC MEME-10 CACACACAC 1.8e-002 2.4e-005 -10.65 0.0 98 492 105 325 0.19919 9.7e-008 245 2 RTCTCAAA DREME-2 GTCTCAAA 2.4e-004 3.1e-007 -14.97 0.0 91 493 43 95 0.18458 1.3e-009 246 2 AAATAAAT DREME-3 AAATAAAT 1.5e-039 2.0e-042 -96.01 0.0 45 493 67 102 0.09128 8.2e-045 246 3 M0436_1.02 (ZNF35)_(Mus_musculus)_(DBD_0.96) TTRTTKDHYN 5.1e-001 6.8e-004 -7.29 0.0 59 491 98 517 0.12016 2.8e-006 245 3 M0437_1.02 (ZNF32)_(Mus_musculus)_(DBD_0.99) TATRTATRT 1.3e-003 1.8e-006 -13.24 0.0 38 492 61 360 0.07724 7.3e-009 245 3 M0633_1.02 DMRT2 KAATKTATWN 7.8e-005 1.0e-007 -16.08 0.0 39 491 78 468 0.07943 4.3e-010 245 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 7.1e-002 9.4e-005 -9.27 0.0 39 489 77 538 0.07975 3.9e-007 244 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 1.0e-006 1.3e-009 -20.42 0.0 47 491 104 540 0.09572 5.5e-012 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 8.3e-003 1.1e-005 -11.42 0.0 67 491 123 556 0.13646 4.5e-008 245 3 M2283_1.02 FOXP1 HWWADGTAAACAAAR 6.0e-004 8.0e-007 -14.04 0.0 54 486 103 515 0.11111 3.3e-009 242 3 M2287_1.02 (HOXC9)_(Mus_musculus)_(DBD_0.98) RGCMATAAATCAB 1.5e-001 2.0e-004 -8.52 0.0 66 488 92 413 0.13525 8.2e-007 243 3 M2385_1.02 FOXP2 RWGTAAACAVR 4.9e0000 6.6e-003 -5.03 0.0 48 490 78 495 0.09796 2.7e-005 244 3 M4452_1.02 BATF TYYYRWWATGASTCA 4.4e0000 5.8e-003 -5.15 0.0 76 486 111 490 0.15638 2.4e-005 242 3 M4567_1.02 FOXA2 NCWRWGTAAACANNN 1.2e0000 1.7e-003 -6.40 0.0 66 486 109 531 0.13580 6.8e-006 242 3 M5287_1.02 ALX4 HTAATYNAATTAN 5.6e-008 7.5e-011 -23.32 0.0 30 488 65 389 0.06148 3.1e-013 243 3 M5291_1.02 ARX YTAATTNRATTAN 2.5e-010 3.3e-013 -28.74 0.0 40 488 76 342 0.08197 1.4e-015 243 3 M5335_1.02 CUX2 ATCGATAHNDTTATYGAT 5.7e-026 7.6e-029 -64.75 0.0 41 483 66 148 0.08489 3.2e-031 241 3 M5348_1.02 DRGX NTAATYHAATTAN 4.3e-005 5.7e-008 -16.68 0.0 30 488 55 348 0.06148 2.4e-010 243 3 M5446_1.02 FOXD4L2 RTAAACA 3.1e0000 4.1e-003 -5.50 0.0 36 494 68 553 0.07287 1.7e-005 246 3 M5460_1.02 FOXL1 RTAAACA 4.9e-003 6.5e-006 -11.95 0.0 36 494 76 536 0.07287 2.6e-008 246 3 M5584_1.02 ISX YTAATCTAATTAR 4.8e-009 6.5e-012 -25.77 0.0 46 488 67 259 0.09426 2.7e-014 243 3 M5637_1.02 MSX1 TAATTGSWWTTTAATTGS 1.6e-001 2.1e-004 -8.47 0.0 59 483 67 303 0.12215 8.7e-007 241 3 M5697_1.02 ONECUT3 DTTATYGATTTTTY 4.4e-006 5.8e-009 -18.96 0.0 49 487 73 323 0.10062 2.4e-011 243 3 M5714_1.02 PHOX2A TAATYYAATTA 7.4e-002 9.9e-005 -9.22 0.0 52 490 71 363 0.10612 4.0e-007 244 3 M5715_1.02 PHOX2B TAATYYAATTA 8.2e-002 1.1e-004 -9.12 0.0 52 490 72 372 0.10612 4.5e-007 244 3 M5740_1.02 POU4F1 ATGMATAATTAATG 1.3e-010 1.8e-013 -29.35 0.0 43 487 88 394 0.08830 7.4e-016 243 3 M5743_1.02 POU4F3 RTGMATWATTAATGAV 1.2e-012 1.6e-015 -34.05 0.0 41 485 86 369 0.08454 6.7e-018 242 3 M5941_1.02 UNCX NTAATYBAATTAN 2.4e-003 3.2e-006 -12.66 0.0 52 488 85 430 0.10656 1.3e-008 243 3 M5981_1.02 ZSCAN4 TTTTCAGKGTGTGCA 2.5e-002 3.3e-005 -10.30 0.0 178 486 172 342 0.36626 1.4e-007 242 3 M6114_1.02 FOXA1 WAWGYAAAYA 5.9e-004 7.9e-007 -14.05 0.0 53 491 101 519 0.10794 3.2e-009 245 3 M6147_1.02 ARID3A TWWAWTTTGATWYYVWTTAATH 1.3e-009 1.7e-012 -27.08 0.0 49 479 82 325 0.10230 7.3e-015 239 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 6.5e-003 8.6e-006 -11.66 0.0 54 488 101 526 0.11066 3.5e-008 243 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 9.4e0000 1.3e-002 -4.38 0.0 54 486 70 396 0.11111 5.2e-005 242 3 M6237_1.02 FOXD3 AAACAAACA 6.8e-007 9.1e-010 -20.82 0.0 38 492 87 508 0.07724 3.7e-012 245 3 M6238_1.02 FOXF1 WAAATAAACAW 4.5e-007 6.0e-010 -21.23 0.0 54 490 113 524 0.11020 2.5e-012 244 3 M6239_1.02 FOXF2 HWADGTAAACA 1.4e-003 1.8e-006 -13.22 0.0 58 490 104 502 0.11837 7.4e-009 244 3 M6241_1.02 FOXJ2 WAAAYAAAYA 1.7e-011 2.2e-014 -31.43 0.0 53 491 121 509 0.10794 9.2e-017 245 3 M6242_1.02 FOXJ3 TAAACAWWAAMMA 8.4e-003 1.1e-005 -11.40 0.0 42 488 77 468 0.08607 4.6e-008 243 3 M6244_1.02 FOXM1 RWAAWCAMWCAAV 1.7e-004 2.3e-007 -15.30 0.0 62 488 125 572 0.12705 9.4e-010 243 3 M6245_1.02 FOXO1 AAAWWVWAAACAAVHH 5.5e-006 7.3e-009 -18.74 0.0 51 485 106 518 0.10515 3.0e-011 242 3 M6246_1.02 FOXO3 MKGWAAACAARYM 1.6e-005 2.1e-008 -17.68 0.0 34 488 81 537 0.06967 8.6e-011 243 3 M6247_1.02 FOXO4 MRTAAACAA 1.7e0000 2.2e-003 -6.11 0.0 36 492 67 529 0.07317 9.0e-006 245 3 M6250_1.02 FOXQ1 AAATAAACAATD 5.1e-003 6.8e-006 -11.90 0.0 49 489 77 404 0.10020 2.8e-008 244 3 M6285_1.02 ONECUT1 WWTATTGATTTWDH 4.7e-005 6.3e-008 -16.58 0.0 51 487 85 401 0.10472 2.6e-010 243 3 M6289_1.02 HOXA9 WCATAAAYYRTH 4.4e-001 5.8e-004 -7.45 0.0 47 489 76 462 0.09611 2.4e-006 244 3 M6296_1.02 HOXB6 KKCATMAATCAWT 9.5e-001 1.3e-003 -6.67 0.0 62 488 71 331 0.12705 5.2e-006 243 3 M6297_1.02 HOXB7 MATYAATCAA 7.4e-005 9.9e-008 -16.13 0.0 45 491 73 367 0.09165 4.0e-010 245 3 M6298_1.02 HOXB8 BMATTAATCAA 3.0e-004 4.0e-007 -14.74 0.0 44 490 66 340 0.08980 1.6e-009 244 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 3.4e-013 4.5e-016 -35.34 0.0 40 486 71 270 0.08230 1.9e-018 242 3 M6329_1.02 LHX3 AAAATTAATTARY 3.4e-004 4.6e-007 -14.59 0.0 64 488 77 296 0.13115 1.9e-009 243 3 M6378_1.02 NKX3-1 WWTAAGTATWTWW 8.1e-008 1.1e-010 -22.95 0.0 50 488 95 428 0.10246 4.4e-013 243 3 M6399_1.02 ONECUT2 DKSWTKWTATKGATTTTWYYT 4.7e-009 6.3e-012 -25.78 0.0 44 480 75 319 0.09167 2.7e-014 239 3 M6426_1.02 POU3F2 CATRAATWWT 7.8e-006 1.0e-008 -18.38 0.0 49 491 98 492 0.09980 4.3e-011 245 3 M6456_1.02 RREB1 DKGKKKGKGGKTGKTTKGGGKT 8.8e0000 1.2e-002 -4.44 0.0 43 479 71 488 0.08977 4.9e-005 239 3 M6546_1.02 ZFHX3 ATTAWTAATTA 5.6e-011 7.5e-014 -30.22 0.0 42 490 76 323 0.08571 3.1e-016 244 ## # 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).