# 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 AGCACCATGGACAGCKCC MEME-1 AGCACCATGGACAGCKCC 1.6e-145 2.2e-148 -339.99 0.0 55 183 418 479 0.30055 2.4e-150 91 1 GSTGGACAGCKCCH MEME-2 GSTGGACAGCKCCH 7.5e-142 1.0e-144 -331.55 0.0 49 187 410 506 0.26203 1.1e-146 93 1 TTCAGCACC MEME-3 TTCAGCACC 4.9e-091 6.7e-094 -214.55 0.0 68 192 371 446 0.35417 7.0e-096 95 2 DCTGTCC DREME-1 GCTGTCC 3.3e-129 4.4e-132 -302.45 0.0 48 194 376 480 0.24742 4.6e-134 96 2 CAGNACC DREME-2 CAGCACC 6.0e-092 8.1e-095 -216.66 0.0 68 194 391 480 0.35052 8.4e-097 96 2 GTGCTGAW DREME-3 GTGCTGAA 4.8e-071 6.5e-074 -168.51 0.0 75 193 345 416 0.38860 6.8e-076 96 3 M0198_1.02 (SOHLH2)_(Mus_musculus)_(DBD_0.84) NGYVCGTGCN 6.0e-002 8.2e-005 -9.41 0.0 11 191 49 403 0.05759 8.6e-007 95 3 M0216_1.02 (NHLH2)_(Mus_musculus)_(DBD_1.00) NGCAGCTGYN 6.7e-001 9.1e-004 -7.00 0.0 89 191 274 485 0.46597 9.6e-006 95 3 M0424_1.02 (SNAI3)_(Mus_musculus)_(DBD_0.75) NNTGACAKNN 1.9e-007 2.6e-010 -22.07 0.0 53 191 233 562 0.27749 2.7e-012 95 3 M1581_1.02 (CIC)_(Mus_musculus)_(DBD_1.00) NNTGCTGACW 7.4e-027 1.0e-029 -66.78 0.0 71 191 331 532 0.37173 1.0e-031 95 3 M2296_1.02 MAFK MHDASTCAGCAWWWW 5.2e-008 7.1e-011 -23.37 0.0 56 186 198 424 0.30108 7.7e-013 92 3 M2299_1.02 (MYF5)_(Mus_musculus)_(DBD_0.90) NRNRRCAGCTGSN 2.6e-005 3.5e-008 -17.17 0.0 40 188 169 510 0.21277 3.7e-010 93 3 M4469_1.02 REST TCCRTGGTGCTGAA 1.1e-120 1.5e-123 -282.78 0.0 65 187 462 550 0.34759 1.7e-125 93 3 M4479_1.02 TCF12 VSAGCAGSTGB 6.9e-001 9.3e-004 -6.98 0.0 82 190 259 490 0.43158 1.0e-005 94 3 M4698_1.02 HNF4A BTGRMCTTTGVMCYB 1.6e-003 2.2e-006 -13.04 0.0 44 186 158 447 0.23656 2.4e-008 92 3 M5621_1.02 MEIS3 SCTGTCAH 1.8e-025 2.4e-028 -63.61 0.0 47 193 256 545 0.24352 2.5e-030 96 3 M5689_1.02 NRL DWWNTGCTGAC 4.2e-012 5.7e-015 -32.80 0.0 70 190 295 542 0.36842 6.1e-017 94 3 M5722_1.02 PKNOX2 TGACACCTGTCA 1.8e0000 2.5e-003 -6.00 0.0 41 189 60 167 0.21693 2.6e-005 94 3 M5934_1.02 TGIF2 TGACASCTGTCA 6.6e-002 9.0e-005 -9.32 0.0 41 189 71 190 0.21693 9.6e-007 94 3 M5935_1.02 TGIF2LX TGACASCTGTCA 4.3e-001 5.8e-004 -7.46 0.0 41 189 62 168 0.21693 6.1e-006 94 3 M6155_1.02 ATF6 GBGSTGACGTGG 7.3e0000 9.9e-003 -4.61 0.0 79 189 114 208 0.41799 1.1e-004 94 3 M6161_1.02 BHLHE41 WSVRKSYCACGTGMHGRRRV 7.4e-003 1.0e-005 -11.51 0.0 77 181 209 372 0.42541 1.1e-007 90 3 M6185_1.02 CXXC1 CGKTGKY 2.4e-011 3.2e-014 -31.07 0.0 34 194 158 482 0.17526 3.3e-016 96 3 M6215_1.02 ESRRB TGACCTTGR 7.0e-002 9.5e-005 -9.27 0.0 94 192 264 437 0.48958 1.0e-006 95 3 M6316_1.02 TCF4 VCAGGTGCD 8.0e-001 1.1e-003 -6.83 0.0 80 192 228 439 0.41667 1.1e-005 95 3 M6330_1.02 MAFA STGCTGACBMYGCAGYHTYCV 6.4e-011 8.6e-014 -30.08 0.0 66 180 284 527 0.36667 9.7e-016 89 3 M6331_1.02 MAFB WGCTGACDS 1.4e-016 1.8e-019 -43.14 0.0 72 192 325 568 0.37500 1.9e-021 95 3 M6332_1.02 MAF KTGCTGAC 3.4e-039 4.6e-042 -95.18 0.0 57 193 337 590 0.29534 4.8e-044 96 3 M6344_1.02 MEIS2 KGACAVCTGTCAA 5.9e-001 8.0e-004 -7.13 0.0 42 188 95 283 0.22340 8.7e-006 93 3 M6353_1.02 MYF6 GCAGSTG 9.7e-002 1.3e-004 -8.93 0.0 88 194 286 513 0.45361 1.4e-006 96 3 M6354_1.02 MYOD1 RACAGSTGS 1.6e-003 2.2e-006 -13.03 0.0 48 192 190 532 0.25000 2.3e-008 95 3 M6355_1.02 MYOG YRACAGCTGCWGC 1.8e-003 2.4e-006 -12.95 0.0 102 188 302 450 0.54255 2.6e-008 93 3 M6366_1.02 NFAT5 MAKGRANTTTTCCRS 9.9e-001 1.3e-003 -6.61 0.0 34 186 89 318 0.18280 1.5e-005 92 3 M6393_1.02 NR4A1 STGACCTTB 1.4e-003 1.9e-006 -13.20 0.0 40 192 137 421 0.20833 2.0e-008 95 3 M6396_1.02 NR5A2 TRRCCTTGRV 1.4e-005 1.9e-008 -17.77 0.0 79 191 272 489 0.41361 2.0e-010 95 3 M6430_1.02 PPARA TGACCTY 2.1e0000 2.9e-003 -5.84 0.0 34 194 130 530 0.17526 3.0e-005 96 3 M6432_1.02 PPARD TGACCTTTVNCCTR 2.6e-025 3.5e-028 -63.23 0.0 33 187 198 506 0.17647 3.7e-030 93 3 M6448_1.02 RELB RGGGRMTTTCCM 9.6e-014 1.3e-016 -36.58 0.0 35 189 178 509 0.18519 1.4e-018 94 3 M6478_1.02 SOX9 ARAACAATGGR 5.0e0000 6.8e-003 -5.00 0.0 46 190 128 389 0.24211 7.2e-005 94 3 M6498_1.02 NR5A1 TGRCCTTGR 1.6e-014 2.2e-017 -38.35 0.0 40 192 202 534 0.20833 2.3e-019 95 3 M6513_1.02 TFAP4 RYCAGCTGYGG 3.3e-006 4.4e-009 -19.24 0.0 50 190 173 421 0.26316 4.7e-011 94 ## # 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).