# 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 AAATCWSWGCH MEME-1 AAATCWSWGCH 1.6e-019 2.1e-022 -49.89 0.0 94 190 372 521 0.49474 2.3e-024 94 1 AMAHAMAHAMAMAMAHAAAHAMAYAMAHAAA MEME-2 AMAHAMAHAMAMAMAHAAAHAMAYAMAHAAA 4.6e0000 6.2e-003 -5.09 0.0 70 170 64 106 0.41176 7.4e-005 84 2 SWGATTW DREME-1 SWGATTT 1.2e-014 1.6e-017 -38.67 0.0 74 194 237 390 0.38144 1.7e-019 96 2 AAAACMA DREME-4 AAAACMA 1.7e-002 2.3e-005 -10.69 0.0 96 194 102 145 0.49485 2.4e-007 96 3 M0105_1.02 (ARID3C)_(Mus_musculus)_(DBD_0.87) NTTTDATHN 3.9e-001 5.2e-004 -7.56 0.0 100 192 282 452 0.52083 5.5e-006 95 3 M0718_1.02 FOXK1 DNRTMAACAH 7.2e0000 9.7e-003 -4.64 0.0 141 191 432 535 0.73822 1.0e-004 95 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 3.6e0000 4.9e-003 -5.32 0.0 161 191 474 525 0.84293 5.2e-005 95 3 M0890_1.02 LHX6 NYAATCAN 4.2e-003 5.7e-006 -12.07 0.0 109 193 365 539 0.56477 6.0e-008 96 3 M1507_1.02 (LCOR)_(Meleagris_gallopavo)_(DBD_1.00) NDWTTNGGNN 5.4e0000 7.2e-003 -4.93 0.0 89 191 237 423 0.46597 7.6e-005 95 3 M1589_1.02 (SOX30)_(Mus_musculus)_(DBD_1.00) NNDNRACAAT 4.4e-003 6.0e-006 -12.03 0.0 105 191 345 519 0.54974 6.3e-008 95 3 M1594_1.02 (SOX12)_(Mus_musculus)_(DBD_1.00) HWTTGTYNNN 1.6e0000 2.2e-003 -6.11 0.0 111 191 360 539 0.58115 2.3e-005 95 3 M1601_1.02 (SOX11)_(Mus_musculus)_(DBD_1.00) WTTGTBNNN 2.5e-003 3.4e-006 -12.58 0.0 98 192 334 533 0.51042 3.6e-008 95 3 M2283_1.02 FOXP1 HWWADGTAAACAAAR 3.4e0000 4.6e-003 -5.38 0.0 100 186 306 489 0.53763 5.0e-005 92 3 M2287_1.02 (HOXC9)_(Mus_musculus)_(DBD_0.98) RGCMATAAATCAB 2.6e-006 3.5e-009 -19.46 0.0 126 188 393 489 0.67021 3.8e-011 93 3 M2310_1.02 RUNX2 MAAACCACARAMMMM 1.5e-001 2.0e-004 -8.52 0.0 78 186 249 474 0.41935 2.2e-006 92 3 M2385_1.02 FOXP2 RWGTAAACAVR 5.9e0000 8.0e-003 -4.83 0.0 164 190 418 454 0.86316 8.5e-005 94 3 M4567_1.02 FOXA2 NMWRWGTAAACANNN 1.5e0000 2.1e-003 -6.17 0.0 168 186 487 511 0.90323 2.3e-005 92 3 M5446_1.02 FOXD4L2 RTAAACA 2.6e-001 3.5e-004 -7.96 0.0 140 194 437 542 0.72165 3.6e-006 96 3 M5460_1.02 FOXL1 RTAAACA 6.5e-001 8.8e-004 -7.04 0.0 140 194 423 527 0.72165 9.1e-006 96 3 M5551_1.02 HOXC12 TTTTATTRC 7.0e-001 9.4e-004 -6.97 0.0 92 192 293 510 0.47917 9.9e-006 95 3 M5557_1.02 HOXD12 GTAATAAAA 1.9e0000 2.5e-003 -5.98 0.0 34 192 125 498 0.17708 2.7e-005 95 3 M5697_1.02 ONECUT3 DTTATYGATTTTTY 5.4e0000 7.3e-003 -4.92 0.0 109 187 188 270 0.58289 7.9e-005 93 3 M6114_1.02 FOXA1 WAWGYAAAYA 5.4e-001 7.3e-004 -7.22 0.0 139 191 419 517 0.72775 7.7e-006 95 3 M6147_1.02 ARID3A TWWAWTTTGATWYYVWTTAATH 6.6e0000 8.9e-003 -4.72 0.0 161 179 271 282 0.89944 1.0e-004 89 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 1.3e0000 1.8e-003 -6.32 0.0 112 188 353 515 0.59574 1.9e-005 93 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 9.3e0000 1.3e-002 -4.38 0.0 140 186 335 404 0.75269 1.4e-004 92 3 M6237_1.02 FOXD3 AAACAAACA 1.2e-001 1.7e-004 -8.70 0.0 146 192 409 482 0.76042 1.7e-006 95 3 M6238_1.02 FOXF1 WAAATAAACAW 2.2e0000 2.9e-003 -5.83 0.0 134 190 362 459 0.70526 3.1e-005 94 3 M6239_1.02 FOXF2 HWADGTAAACA 3.2e-001 4.3e-004 -7.74 0.0 88 190 265 468 0.46316 4.6e-006 94 3 M6241_1.02 FOXJ2 WAAAYAAAYA 6.9e-001 9.3e-004 -6.98 0.0 135 191 382 482 0.70681 9.8e-006 95 3 M6242_1.02 FOXJ3 TAAACAWWAAMMA 1.8e-002 2.4e-005 -10.64 0.0 114 188 299 412 0.60638 2.6e-007 93 3 M6244_1.02 FOXM1 RWAAWCAMWCAAV 5.9e-005 8.0e-008 -16.34 0.0 120 188 420 553 0.63830 8.6e-010 93 3 M6245_1.02 FOXO1 AAAWWVWAAACAAVHH 9.2e-002 1.2e-004 -8.99 0.0 115 185 363 502 0.62162 1.3e-006 92 3 M6247_1.02 FOXO4 MRTAAACAA 4.2e0000 5.6e-003 -5.18 0.0 122 192 360 502 0.63542 6.0e-005 95 3 M6258_1.02 GATA6 NWGATAA 2.0e-002 2.7e-005 -10.51 0.0 108 194 364 549 0.55670 2.9e-007 96 3 M6262_1.02 GFI1B WGCMGTGATTT 3.6e-018 4.9e-021 -46.77 0.0 82 190 355 555 0.43158 5.2e-023 94 3 M6263_1.02 GFI1 RCWSTGATTT 1.2e-014 1.7e-017 -38.64 0.0 101 191 415 583 0.52880 1.7e-019 95 3 M6297_1.02 HOXB7 MATYAATCAA 3.1e-001 4.2e-004 -7.77 0.0 135 191 306 378 0.70681 4.4e-006 95 3 M6298_1.02 HOXB8 BMATTAATCAA 8.6e0000 1.2e-002 -4.46 0.0 118 190 247 344 0.62105 1.2e-004 94 3 M6299_1.02 HOXC6 AAAGTAATAAATCAT 2.1e-001 2.9e-004 -8.15 0.0 106 186 168 235 0.56989 3.2e-006 92 3 M6301_1.02 HOXD10 AATTAAARCA 3.9e-002 5.2e-005 -9.86 0.0 149 191 447 517 0.78010 5.5e-007 95 3 M6304_1.02 HOXD9 HMATNAAWYT 2.7e0000 3.6e-003 -5.62 0.0 35 191 127 495 0.18325 3.8e-005 95 3 M6401_1.02 OTX2 HYYTAATCCBWKHDM 4.0e0000 5.4e-003 -5.21 0.0 52 186 151 410 0.27957 5.9e-005 92 3 M6413_1.02 PBX2 VMATCAATCAMWTYM 1.6e-002 2.1e-005 -10.76 0.0 128 186 415 527 0.68817 2.3e-007 92 3 M6418_1.02 PITX2 DBTAATCCMA 6.4e0000 8.7e-003 -4.75 0.0 61 191 211 532 0.31937 9.1e-005 95 3 M6471_1.02 SOX13 YATTGTTY 1.3e-001 1.8e-004 -8.62 0.0 95 193 302 507 0.49223 1.9e-006 96 3 M6477_1.02 SOX5 WAACAATR 2.8e0000 3.8e-003 -5.57 0.0 89 193 288 525 0.46114 4.0e-005 96 3 M6490_1.02 SRY DAAACAAWR 1.7e0000 2.3e-003 -6.07 0.0 110 192 352 533 0.57292 2.4e-005 95 3 M6517_1.02 TFE3 RGTCAYGTGV 3.4e0000 4.6e-003 -5.37 0.0 7 191 32 404 0.03665 4.9e-005 95 ## # 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).