# 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 GAWGGAWGGAWGGAWGGAWGG MEME-1 GAWGGAWGGAWGGAWGGAWGG 1.7e-047 2.2e-050 -114.33 0.0 142 480 313 500 0.29583 9.3e-053 239 1 GGAWGGAWGGAWGGAWGGAWG MEME-2 GGAWGGAWGGAWGGAWGGAWG 1.4e-050 1.9e-053 -121.40 0.0 152 480 355 551 0.31667 7.9e-056 239 1 TCCWTCCWTCCW MEME-3 TCCWTCCWTCCW 4.1e-042 5.5e-045 -101.92 0.0 127 489 319 591 0.25971 2.2e-047 244 1 ARAGRRARRGARRGAR MEME-4 ARAGRRARRGARRGAR 1.1e-019 1.4e-022 -50.29 0.0 109 485 208 474 0.22474 6.0e-025 242 1 ATGGATGGATG MEME-5 ATGGATGGATG 9.1e-007 1.2e-009 -20.53 0.0 240 490 205 298 0.48980 5.0e-012 244 1 TGGATGGAT MEME-6 TGGATGGAT 6.1e-003 8.1e-006 -11.73 0.0 268 492 204 291 0.54472 3.3e-008 245 1 AARRRAAAGAAA MEME-7 AARRRAAAGAAA 3.1e-012 4.2e-015 -33.11 0.0 131 489 184 394 0.26789 1.7e-017 244 2 TCCWTCCW DREME-1 TCCATCCA 3.0e-022 4.0e-025 -56.17 0.0 223 493 282 390 0.45233 1.6e-027 246 2 TCTAYYCA DREME-2 TCTATCCA 4.8e0000 6.3e-003 -5.06 0.0 255 493 136 207 0.51724 2.6e-005 246 2 GGACRGA DREME-3 GGACRGA 2.9e0000 3.9e-003 -5.54 0.0 86 494 61 210 0.17409 1.6e-005 246 2 TRGATGAA DREME-4 TGGATGAA 9.2e-001 1.2e-003 -6.70 0.0 251 493 135 203 0.50913 5.0e-006 246 2 CCTCCCTC DREME-7 CCTCCCTC 1.5e-009 1.9e-012 -26.97 0.0 173 493 118 187 0.35091 7.9e-015 246 3 M1882_1.02 IRF1 AAANNGAAAGTGAAASYRRRN 1.8e-003 2.5e-006 -12.92 0.0 110 480 157 452 0.22917 1.0e-008 239 3 M1915_1.02 (ZNF76)_(Xenopus_laevis)_(DBD_0.84) KCRWKGMATBMTGGGARDTV 5.5e-006 7.2e-009 -18.74 0.0 175 481 283 566 0.36383 3.0e-011 240 3 M2273_1.02 E2F6 RGGCGGGARRV 6.2e-004 8.2e-007 -14.01 0.0 196 490 301 579 0.40000 3.4e-009 244 3 M2307_1.02 PRDM1 DRAAAGTGAAAGTGR 5.5e-007 7.4e-010 -21.03 0.0 104 486 186 542 0.21399 3.0e-012 242 3 M2390_1.02 EHF SAGGAAGK 9.8e0000 1.3e-002 -4.34 0.0 83 493 125 534 0.16836 5.4e-005 246 3 M4453_1.02 BCL11A ADGRGGAASTGAAAV 2.1e-003 2.8e-006 -12.78 0.0 82 486 152 579 0.16872 1.2e-008 242 3 M4545_1.02 ZNF683 DRAAAGTGAAAGTGV 3.2e-003 4.2e-006 -12.38 0.0 100 486 165 535 0.20576 1.7e-008 242 3 M4604_1.02 ZNF263 RRGGAGGASGVVGRGGRGGRG 1.2e-007 1.7e-010 -22.52 0.0 74 480 156 578 0.15417 7.0e-013 239 3 M5865_1.02 SPIC NAAAAGVGGAAGTA 3.7e-004 4.9e-007 -14.52 0.0 81 487 143 533 0.16632 2.0e-009 243 3 M6119_1.02 SPI1 RAAAAGAGGAAGTGV 4.6e-002 6.1e-005 -9.70 0.0 38 486 76 529 0.07819 2.5e-007 242 3 M6154_1.02 ATF5 TAAGGRAGARGK 5.5e-011 7.3e-014 -30.25 0.0 155 489 285 597 0.31697 3.0e-016 244 3 M6278_1.02 HLTF KANKGCTGSMAM 8.5e-001 1.1e-003 -6.79 0.0 121 489 196 594 0.24744 4.6e-006 244 3 M6291_1.02 HOXA1 CATCCATCMA 1.1e-001 1.5e-004 -8.80 0.0 169 491 224 496 0.34420 6.2e-007 245 3 M6295_1.02 HOXB1 CCATCMATCW 2.0e-002 2.7e-005 -10.52 0.0 147 491 213 523 0.29939 1.1e-007 245 3 M6308_1.02 IRF2 SGAAAGYGAAASYV 7.7e0000 1.0e-002 -4.58 0.0 149 487 187 478 0.30595 4.2e-005 243 3 M6309_1.02 IRF3 GGAAAGBGAAASBRRRA 1.1e-004 1.4e-007 -15.75 0.0 116 484 179 493 0.23967 6.0e-010 241 3 M6311_1.02 IRF5 KAAAGGRAARCMAAAWSWGA 2.3e-007 3.0e-010 -21.92 0.0 123 481 136 308 0.25572 1.3e-012 240 3 M6313_1.02 IRF8 GRGRAAVTGAAASYR 2.1e0000 2.8e-003 -5.89 0.0 32 486 62 530 0.06584 1.1e-005 242 3 M6336_1.02 MAZ RGGGDRGGGAGGGRGGG 7.0e-005 9.3e-008 -16.20 0.0 118 484 209 583 0.24380 3.8e-010 241 3 M6338_1.02 NR3C2 YMCHWCAACCWGKHCTD 6.5e-001 8.7e-004 -7.05 0.0 246 484 340 563 0.50826 3.6e-006 241 3 M6419_1.02 PKNOX1 MATCARTCAABYB 4.0e0000 5.4e-003 -5.23 0.0 46 488 79 522 0.09426 2.2e-005 243 3 M6485_1.02 SPIB ARAAASMGGAAS 3.2e-005 4.3e-008 -16.96 0.0 93 489 165 544 0.19018 1.8e-010 244 ## # 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).