# 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 CACACACACACACACACACACACACACACAC MEME-1 CACACACACACACACACACACACACACACAC 1.3e-007 1.7e-010 -22.49 0.0 112 470 42 62 0.23830 7.3e-013 234 1 GATGACRTCACC MEME-9 GATGACRTCACC 2.4e-002 3.3e-005 -10.33 0.0 223 489 170 277 0.45603 1.3e-007 244 1 RTGACTCAB MEME-10 RTGACTCAB 1.9e-008 2.5e-011 -24.42 0.0 176 492 111 174 0.35772 1.0e-013 245 2 TGAGTCAB DREME-1 TGAGTCAB 5.8e-010 7.7e-013 -27.89 0.0 227 493 101 125 0.46045 3.1e-015 246 2 TGACMTCA DREME-4 TGACMTCA 3.3e-004 4.4e-007 -14.63 0.0 325 493 106 118 0.65923 1.8e-009 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 2.9e-002 3.9e-005 -10.15 0.0 223 491 302 535 0.45418 1.6e-007 245 3 M0719_1.02 FOXG1 RTAAACAW 1.1e0000 1.4e-003 -6.55 0.0 105 493 132 435 0.21298 5.8e-006 246 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 5.2e0000 6.9e-003 -4.98 0.0 131 491 183 526 0.26680 2.8e-005 245 3 M0887_1.02 HOXA2 NNYRAYBDN 3.0e0000 4.0e-003 -5.52 0.0 70 492 43 156 0.14228 1.6e-005 245 3 M0896_1.02 VENTX TTAATTAG 7.0e0000 9.4e-003 -4.67 0.0 77 493 101 438 0.15619 3.8e-005 246 3 M0949_1.02 (AC012531.1)_(Mus_musculus)_(DBD_1.00) NTAATDR 6.2e0000 8.3e-003 -4.79 0.0 70 494 98 467 0.14170 3.4e-005 246 3 M1545_1.02 GMEB1 NNNRCGTNN 3.5e0000 4.7e-003 -5.36 0.0 426 492 451 487 0.86585 1.9e-005 245 3 M1863_1.02 FOXD1 GTAAACAW 7.0e0000 9.3e-003 -4.68 0.0 105 493 137 468 0.21298 3.8e-005 246 3 M2278_1.02 FOS DVTGASTCATB 2.6e-005 3.4e-008 -17.19 0.0 218 490 269 453 0.44490 1.4e-010 244 3 M2289_1.02 JUN DDRATGATGTMAT 2.1e-004 2.8e-007 -15.08 0.0 284 488 317 440 0.58197 1.2e-009 243 3 M2292_1.02 JUND DRTGASTCATS 3.1e-006 4.2e-009 -19.29 0.0 216 490 266 445 0.44082 1.7e-011 244 3 M4526_1.02 SMARCC1 DSRVDGTGASTCABV 5.5e-001 7.3e-004 -7.22 0.0 154 486 203 488 0.31687 3.0e-006 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 9.4e-006 1.3e-008 -18.20 0.0 215 487 267 449 0.44148 5.2e-011 243 3 M4567_1.02 FOXA2 NCWRWGTAAACANNN 1.1e-001 1.5e-004 -8.83 0.0 182 486 244 507 0.37449 6.1e-007 242 3 M4619_1.02 FOSL1 BGGTGASTCAK 6.3e-006 8.4e-009 -18.59 0.0 216 490 261 436 0.44082 3.4e-011 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 1.0e-004 1.4e-007 -15.79 0.0 222 486 271 451 0.45679 5.7e-010 242 3 M4629_1.02 NFE2 VRTGACTCAGCANWWYB 2.4e-003 3.2e-006 -12.66 0.0 210 484 227 395 0.43388 1.3e-008 241 3 M4681_1.02 BACH2 TGCTGAGTCA 3.1e0000 4.1e-003 -5.50 0.0 143 491 169 438 0.29124 1.7e-005 245 3 M4930_1.02 (NPAS4)_(Drosophila_melanogaster)_(DBD_0.61) RADTCGTGACT 1.4e0000 1.8e-003 -6.32 0.0 60 490 82 410 0.12245 7.4e-006 244 3 M5292_1.02 ATF4 GKATGAYGCAATM 2.1e0000 2.8e-003 -5.87 0.0 286 488 290 422 0.58607 1.2e-005 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 2.1e-004 2.8e-007 -15.07 0.0 261 487 201 283 0.53593 1.2e-009 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.3e-004 1.7e-007 -15.59 0.0 269 487 119 150 0.55236 7.0e-010 243 3 M5310_1.02 BSX BTAATBRS 1.3e0000 1.7e-003 -6.35 0.0 109 493 151 493 0.22110 7.1e-006 246 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 6.9e-002 9.3e-005 -9.28 0.0 269 487 202 291 0.55236 3.8e-007 243 3 M5349_1.02 DUXA NTRAYYTAATCAN 3.7e0000 4.9e-003 -5.31 0.0 226 488 258 461 0.46311 2.0e-005 243 3 M5390_1.02 EN1 VBTAATTRSB 3.1e0000 4.2e-003 -5.48 0.0 7 491 21 503 0.01426 1.7e-005 245 3 M5446_1.02 FOXD4L2 GTAAACA 4.4e-001 5.9e-004 -7.43 0.0 176 494 245 542 0.35628 2.4e-006 246 3 M5460_1.02 FOXL1 RTAAACA 2.9e-002 3.9e-005 -10.16 0.0 176 494 241 517 0.35628 1.6e-007 246 3 M5555_1.02 HOXD11 RTCGTAAAAH 4.6e0000 6.1e-003 -5.10 0.0 157 491 188 456 0.31976 2.5e-005 245 3 M5587_1.02 JDP2 ATGASTCAT 3.0e-005 4.1e-008 -17.02 0.0 144 492 181 411 0.29268 1.7e-010 245 3 M5772_1.02 RAX2 BTAATTRR 8.3e0000 1.1e-002 -4.50 0.0 7 493 20 500 0.01420 4.6e-005 246 3 M5782_1.02 RHOXF1 GGATDAKCC 9.9e0000 1.3e-002 -4.33 0.0 312 492 382 535 0.63415 5.4e-005 245 3 M5873_1.02 TBR1 AGGTGTGAAA 7.2e0000 9.6e-003 -4.65 0.0 7 491 21 533 0.01426 3.9e-005 245 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 1.9e-006 2.5e-009 -19.79 0.0 225 489 215 333 0.46012 1.0e-011 244 3 M6114_1.02 FOXA1 WAWGYAAAYA 1.9e0000 2.5e-003 -5.99 0.0 121 491 166 500 0.24644 1.0e-005 245 3 M6152_1.02 ATF1 VTGACGTCAV 3.9e-002 5.2e-005 -9.86 0.0 225 491 277 483 0.45825 2.1e-007 245 3 M6167_1.02 CDX1 HCATAAAD 1.8e-001 2.4e-004 -8.35 0.0 193 493 274 557 0.39148 9.6e-007 246 3 M6180_1.02 CREB1 RTGACGTMA 1.8e-003 2.4e-006 -12.95 0.0 286 492 381 546 0.58130 9.7e-009 245 3 M6181_1.02 CREM CRVTGACGTCA 5.7e-002 7.6e-005 -9.48 0.0 218 490 285 513 0.44490 3.1e-007 244 3 M6197_1.02 E4F1 YGTKACGTC 4.3e-002 5.8e-005 -9.75 0.0 266 492 303 461 0.54065 2.4e-007 245 3 M6228_1.02 FOSB CTGACTCAYV 2.6e-001 3.5e-004 -7.97 0.0 177 491 251 547 0.36049 1.4e-006 245 3 M6277_1.02 HLF SKRTTACRYAAYC 2.0e0000 2.7e-003 -5.92 0.0 292 488 302 432 0.59836 1.1e-005 243 3 M6331_1.02 MAFB WGCTGACDS 9.3e0000 1.2e-002 -4.38 0.0 306 492 417 596 0.62195 5.1e-005 245 3 M6333_1.02 MAFG MATGACT 1.5e-003 2.1e-006 -13.09 0.0 220 494 321 568 0.44534 8.4e-009 246 3 M6359_1.02 NFE2L1 NATGACD 2.0e-001 2.6e-004 -8.24 0.0 222 494 314 571 0.44939 1.1e-006 246 3 M6360_1.02 NFE2L2 VRTGACTCAGCA 9.3e0000 1.2e-002 -4.39 0.0 13 489 33 580 0.02658 5.1e-005 244 3 M6368_1.02 NFIL3 VKVMVTTACRTAAY 7.6e0000 1.0e-002 -4.59 0.0 181 487 186 396 0.37166 4.2e-005 243 3 M6376_1.02 NKX2-5 TYAAGTG 5.8e-002 7.8e-005 -9.46 0.0 172 494 261 580 0.34818 3.2e-007 246 ## # 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).