# 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 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTWK MEME-1 TTTATTTATTTATTTATTTATTTATTTATTTATTTATTTATTTWK 5.0e-059 6.7e-062 -140.86 0.0 16 456 58 84 0.03509 2.9e-064 227 1 WGCAATTCCGCTCMY MEME-2 WGCAATTCCGCTCMY 7.0e-042 9.4e-045 -101.38 0.0 84 486 218 476 0.17284 3.9e-047 242 1 AGACRGAGTCTCRCTCTGTYRC MEME-3 AGACRGAGTCTCRCTCTGTYRC 2.9e-002 3.8e-005 -10.17 0.0 95 479 46 111 0.19833 1.6e-007 239 1 WGCAATTCCNGCTCMC MEME-4 WGCAATTCCNGCTCMC 1.7e-008 2.3e-011 -24.49 0.0 163 485 180 338 0.33608 9.5e-014 242 1 WAWAAAWAAAWAAAAAAAHAAA MEME-5 WAWAAAWAAAWAAAAAAAHAAA 4.9e-021 6.6e-024 -53.38 0.0 23 479 67 294 0.04802 2.8e-026 239 1 CCCKCCCYCSCYYCCBCCSYYC MEME-7 CCCKCCCYCSCYYCCBCCSYYC 1.5e0000 1.9e-003 -6.24 0.0 79 479 115 470 0.16493 8.1e-006 239 1 CARCCTCCRCCTCCYGGGTTCAAGYRATYCT MEME-8 CARCCTCCRCCTCCYGGGTTCAAGYRATYCT 1.9e0000 2.5e-003 -5.99 0.0 258 470 72 94 0.54894 1.1e-005 234 2 GAGCGDA DREME-1 GAGCGKA 2.1e-025 2.8e-028 -63.43 0.0 82 494 103 196 0.16599 1.1e-030 246 2 AATTGY DREME-2 AATTGC 4.2e-013 5.6e-016 -35.12 0.0 77 495 92 237 0.15556 2.3e-018 247 2 AAATAAAT DREME-3 AAATAAAT 2.6e-036 3.5e-039 -88.55 0.0 47 493 67 106 0.09533 1.4e-041 246 2 CAGCTC DREME-7 CAGCTC 4.7e0000 6.3e-003 -5.07 0.0 179 495 139 289 0.36162 2.6e-005 247 2 GAGCARA DREME-8 GAGCARA 5.6e-009 7.5e-012 -25.62 0.0 152 494 103 177 0.30769 3.0e-014 246 3 M0104_1.02 (ARID3B)_(Mus_musculus)_(DBD_0.99) AWATTAATWAN 8.8e0000 1.2e-002 -4.45 0.0 48 490 72 455 0.09796 4.8e-005 244 3 M0398_1.02 (ZSCAN10)_(Mus_musculus)_(DBD_0.82) NGKRAGTGCNN 2.7e-001 3.6e-004 -7.93 0.0 128 490 202 578 0.26122 1.5e-006 244 3 M0436_1.02 (ZNF35)_(Mus_musculus)_(DBD_0.96) TTRTTKDHYN 1.7e-003 2.2e-006 -13.01 0.0 47 491 95 547 0.09572 9.2e-009 245 3 M0437_1.02 (ZNF32)_(Mus_musculus)_(DBD_0.99) TATRTATRT 4.7e-002 6.3e-005 -9.67 0.0 30 492 53 413 0.06098 2.6e-007 245 3 M0608_1.02 MLL NNNRSCGNDN 5.6e-005 7.5e-008 -16.41 0.0 95 491 135 419 0.19348 3.0e-010 245 3 M0633_1.02 DMRT2 KAATKTATWN 1.4e-003 1.9e-006 -13.19 0.0 41 491 77 464 0.08350 7.6e-009 245 3 M0718_1.02 FOXK1 NNRTMAACAH 9.6e-002 1.3e-004 -8.96 0.0 33 491 69 548 0.06721 5.2e-007 245 3 M0719_1.02 FOXG1 RTAAACAW 2.8e-002 3.7e-005 -10.20 0.0 73 493 104 426 0.14807 1.5e-007 246 3 M0728_1.02 (FOXJ1)_(Mus_musculus)_(DBD_1.00) NRTAAACAAANN 2.4e-004 3.2e-007 -14.94 0.0 39 489 84 530 0.07975 1.3e-009 244 3 M0736_1.02 (FOXK2)_(Mus_musculus)_(DBD_0.90) RTMAACAA 1.1e-001 1.5e-004 -8.80 0.0 73 493 120 524 0.14807 6.1e-007 246 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 1.0e-005 1.4e-008 -18.10 0.0 47 491 100 532 0.09572 5.6e-011 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 3.6e-002 4.7e-005 -9.96 0.0 65 491 115 542 0.13238 1.9e-007 245 3 M0891_1.02 TLX2 NTAAWNNNNN 8.9e-001 1.2e-003 -6.74 0.0 37 491 53 372 0.07536 4.8e-006 245 3 M0896_1.02 VENTX TTAATTAG 2.4e-001 3.1e-004 -8.07 0.0 43 493 72 465 0.08722 1.3e-006 246 3 M0906_1.02 (VTN)_(Mus_musculus)_(DBD_0.79) NMTTAATTAR 8.7e-003 1.2e-005 -11.37 0.0 41 491 65 385 0.08350 4.7e-008 245 3 M1582_1.02 (HMG20B)_(Mus_musculus)_(DBD_0.94) NWAWATAATWN 9.3e-002 1.2e-004 -8.99 0.0 34 490 62 457 0.06939 5.1e-007 244 3 M1605_1.02 (SOX1)_(Mus_musculus)_(DBD_1.00) ATTSWHNNNN 1.2e-001 1.6e-004 -8.76 0.0 49 491 92 549 0.09980 6.4e-007 245 3 M2283_1.02 FOXP1 HWWADGTAAACAAAR 1.0e-001 1.4e-004 -8.90 0.0 40 486 75 508 0.08230 5.6e-007 242 3 M2287_1.02 (HOXC9)_(Mus_musculus)_(DBD_0.98) RGCCATAAATCAB 6.8e-003 9.1e-006 -11.61 0.0 58 488 95 453 0.11885 3.8e-008 243 3 M2385_1.02 FOXP2 RWGTAAACAVR 3.9e-001 5.2e-004 -7.56 0.0 34 490 64 497 0.06939 2.1e-006 244 3 M2388_1.02 SREBF2 RTGGGGTGAY 4.1e0000 5.4e-003 -5.22 0.0 229 491 280 502 0.46640 2.2e-005 245 3 M4567_1.02 FOXA2 NCWRWGTAAACANNN 4.9e-007 6.6e-010 -21.14 0.0 58 486 117 511 0.11934 2.7e-012 242 3 M5287_1.02 ALX4 HTAATYNAATTAN 2.2e-010 2.9e-013 -28.87 0.0 40 488 90 440 0.08197 1.2e-015 243 3 M5291_1.02 ARX YTAATTNRATTAN 1.1e-010 1.5e-013 -29.54 0.0 30 488 72 406 0.06148 6.1e-016 243 3 M5300_1.02 BARX1 TAATBGNTWTTTAATBG 6.0e-001 8.0e-004 -7.13 0.0 46 484 65 382 0.09504 3.3e-006 241 3 M5335_1.02 CUX2 ATCGATAHNDTTATYGAT 1.7e-027 2.3e-030 -68.26 0.0 33 483 64 161 0.06832 9.4e-033 241 3 M5348_1.02 DRGX NTAATYHAATTAN 1.4e-008 1.9e-011 -24.68 0.0 38 488 79 407 0.07787 7.9e-014 243 3 M5446_1.02 FOXD4L2 GTAAACA 5.4e-004 7.2e-007 -14.14 0.0 32 494 74 548 0.06478 2.9e-009 246 3 M5460_1.02 FOXL1 RTAAACA 2.2e-004 3.0e-007 -15.02 0.0 42 494 87 518 0.08502 1.2e-009 246 3 M5584_1.02 ISX YTAATCTAATTAR 1.4e-010 1.8e-013 -29.33 0.0 38 488 73 330 0.07787 7.6e-016 243 3 M5637_1.02 MSX1 TAATTGSWWTTTAATTGS 4.3e-005 5.7e-008 -16.67 0.0 47 483 77 377 0.09731 2.4e-010 241 3 M5697_1.02 ONECUT3 DTTATYGATTTTTY 1.9e-006 2.5e-009 -19.82 0.0 47 487 85 406 0.09651 1.0e-011 243 3 M5704_1.02 PAX3 TAATYRATTA 1.0e-002 1.4e-005 -11.20 0.0 59 491 71 309 0.12016 5.6e-008 245 3 M5714_1.02 PHOX2A TAATYYAATTA 5.9e-007 7.9e-010 -20.96 0.0 40 490 79 419 0.08163 3.2e-012 244 3 M5715_1.02 PHOX2B TAATBYAATTA 9.9e-009 1.3e-011 -25.05 0.0 40 490 84 426 0.08163 5.4e-014 244 3 M5740_1.02 POU4F1 ATGMATAATTAATG 1.2e-009 1.6e-012 -27.14 0.0 37 487 81 419 0.07598 6.7e-015 243 3 M5743_1.02 POU4F3 RTGMATWATTAATGAV 2.0e-010 2.7e-013 -28.94 0.0 35 485 80 416 0.07216 1.1e-015 242 3 M5941_1.02 UNCX NTAATYBAATTAN 4.5e-007 6.0e-010 -21.23 0.0 42 488 89 473 0.08607 2.5e-012 243 3 M6114_1.02 FOXA1 WAWGYAAAYA 6.4e-003 8.5e-006 -11.67 0.0 59 491 104 504 0.12016 3.5e-008 245 3 M6141_1.02 ALX1 TAATBYAATTAB 3.0e-002 4.0e-005 -10.13 0.0 43 489 74 453 0.08793 1.6e-007 244 3 M6147_1.02 ARID3A TWWAWTTTGATWYYVWTTAATH 9.2e-006 1.2e-008 -18.22 0.0 47 479 78 369 0.09812 5.1e-011 239 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 6.9e-005 9.1e-008 -16.21 0.0 46 488 95 517 0.09426 3.8e-010 243 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 6.3e-002 8.3e-005 -9.39 0.0 44 486 73 440 0.09053 3.4e-007 242 3 M6237_1.02 FOXD3 AAACAAACA 1.7e-001 2.3e-004 -8.37 0.0 56 492 98 525 0.11382 9.4e-007 245 3 M6238_1.02 FOXF1 WAAATAAACAW 1.6e-001 2.1e-004 -8.48 0.0 46 490 80 487 0.09388 8.5e-007 244 3 M6239_1.02 FOXF2 HWADGTAAACA 1.4e-001 1.9e-004 -8.59 0.0 44 490 78 492 0.08980 7.6e-007 244 3 M6241_1.02 FOXJ2 WAAAYAAACA 4.7e-006 6.2e-009 -18.89 0.0 27 491 67 498 0.05499 2.5e-011 245 3 M6242_1.02 FOXJ3 TAAACAWWAAMMA 1.8e-005 2.4e-008 -17.54 0.0 44 488 83 435 0.09016 1.0e-010 243 3 M6244_1.02 FOXM1 RWAAWCAMWCAAV 4.4e-005 5.8e-008 -16.66 0.0 46 488 98 535 0.09426 2.4e-010 243 3 M6245_1.02 FOXO1 AAAWWVWAAACAAVHH 3.7e-006 5.0e-009 -19.12 0.0 33 485 78 508 0.06804 2.0e-011 242 3 M6246_1.02 FOXO3 MKGWAAACAARYM 2.5e-004 3.3e-007 -14.92 0.0 42 488 88 521 0.08607 1.4e-009 243 3 M6247_1.02 FOXO4 MRTAAACAA 1.4e-001 1.8e-004 -8.61 0.0 42 492 78 521 0.08537 7.5e-007 245 3 M6250_1.02 FOXQ1 AAATAAACAATD 1.5e-004 2.0e-007 -15.44 0.0 47 489 81 417 0.09611 8.1e-010 244 3 M6269_1.02 HBP1 AYYCATTGA 6.5e-001 8.7e-004 -7.05 0.0 72 492 110 493 0.14634 3.6e-006 245 3 M6285_1.02 ONECUT1 WWTATTGATTTWDH 3.0e-007 4.0e-010 -21.64 0.0 31 487 70 433 0.06366 1.6e-012 243 3 M6289_1.02 HOXA9 WCATAAAYYRTH 2.5e-001 3.4e-004 -8.00 0.0 47 489 79 475 0.09611 1.4e-006 244 3 M6296_1.02 HOXB6 KKCATMAATCAWY 1.5e-005 2.0e-008 -17.75 0.0 46 488 74 357 0.09426 8.1e-011 243 3 M6297_1.02 HOXB7 MATYAATCAA 3.0e-009 3.9e-012 -26.26 0.0 39 491 81 407 0.07943 1.6e-014 245 3 M6298_1.02 HOXB8 BMATTAATCAA 3.5e-006 4.7e-009 -19.18 0.0 46 490 81 393 0.09388 1.9e-011 244 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 3.7e-020 4.9e-023 -51.37 0.0 42 486 89 299 0.08642 2.0e-025 242 3 M6329_1.02 LHX3 AAAATTAATTARY 6.4e-004 8.5e-007 -13.98 0.0 46 488 74 384 0.09426 3.5e-009 243 3 M6348_1.02 MTF1 MGKGCCGTGYGCAAARS 2.3e0000 3.0e-003 -5.80 0.0 188 484 201 407 0.38843 1.3e-005 241 3 M6378_1.02 NKX3-1 WWTAAGTATWTWW 2.3e-006 3.0e-009 -19.62 0.0 48 488 92 448 0.09836 1.2e-011 243 3 M6399_1.02 ONECUT2 DKSWTKWTATKGATTTTWYYT 8.8e-013 1.2e-015 -34.39 0.0 52 480 100 372 0.10833 4.9e-018 239 3 M6413_1.02 PBX2 VMATCAATCAMWTYM 5.3e-006 7.0e-009 -18.77 0.0 42 486 91 508 0.08642 2.9e-011 242 3 M6417_1.02 POU1F1 RWATATTCATKAR 1.5e-001 2.0e-004 -8.53 0.0 36 488 66 475 0.07377 8.1e-007 243 3 M6426_1.02 POU3F2 CATRAATWWT 3.2e-006 4.3e-009 -19.27 0.0 43 491 93 511 0.08758 1.7e-011 245 3 M6438_1.02 PROP1 RASHAATTAAHWTVR 1.3e0000 1.8e-003 -6.33 0.0 48 486 78 474 0.09877 7.4e-006 242 3 M6510_1.02 TEF TGTTTATRTAAMTK 1.9e0000 2.6e-003 -5.97 0.0 43 487 73 497 0.08830 1.1e-005 243 3 M6546_1.02 ZFHX3 RTTAWTAATTA 2.0e-009 2.6e-012 -26.67 0.0 46 490 87 387 0.09388 1.1e-014 244 ## # 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).