# 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 TGTGTGTGTGTGTGTGTGTGTGTGTGT MEME-1 TGTGTGTGTGTGTGTGTGTGTGTGTGT 2.9e-003 3.9e-006 -12.46 0.0 216 474 47 58 0.45570 1.6e-008 236 2 TGAGTCAB DREME-1 TGAGTCAB 1.8e-010 2.5e-013 -29.03 0.0 271 493 128 150 0.54970 1.0e-015 246 2 HATAAA DREME-2 MATAAA 3.8e0000 5.2e-003 -5.27 0.0 153 495 141 338 0.30909 2.1e-005 247 2 TGACHTCA DREME-3 TGACMTCA 2.8e-004 3.7e-007 -14.80 0.0 325 493 109 122 0.65923 1.5e-009 246 2 AGATAA DREME-4 AGATAA 2.9e-001 3.9e-004 -7.85 0.0 177 495 92 173 0.35758 1.6e-006 247 2 AAGTGCY DREME-7 AAGTGCY 5.8e-001 7.8e-004 -7.16 0.0 72 494 42 139 0.14575 3.2e-006 246 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 1.7e-003 2.3e-006 -13.00 0.0 193 491 277 539 0.39308 9.3e-009 245 3 M0415_1.02 (KLF9)_(Mus_musculus)_(DBD_1.00) VTAACGGN 6.0e0000 8.0e-003 -4.83 0.0 381 493 434 514 0.77282 3.3e-005 246 3 M0719_1.02 FOXG1 RTAAACAW 1.8e-001 2.4e-004 -8.32 0.0 105 493 139 450 0.21298 9.9e-007 246 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 1.5e0000 2.1e-003 -6.18 0.0 133 491 189 530 0.27088 8.4e-006 245 3 M0747_1.02 (FOXL2)_(Mus_musculus)_(DBD_0.70) WNNRTAAAYA 3.3e-002 4.4e-005 -10.02 0.0 161 491 236 545 0.32790 1.8e-007 245 3 M0756_1.02 (FOXN3)_(Strongylocentrotus_purpuratus)_(DBD_0.44) NNHMACANN 9.0e0000 1.2e-002 -4.42 0.0 106 492 146 503 0.21545 4.9e-005 245 3 M0892_1.02 EMX1 NYTAATKAVN 3.5e-001 4.8e-004 -7.65 0.0 111 491 158 498 0.22607 1.9e-006 245 3 M0896_1.02 VENTX TTAATTAG 4.7e0000 6.4e-003 -5.06 0.0 167 493 192 444 0.33874 2.6e-005 246 3 M0897_1.02 HOXB13 DTTWAYDRBN 9.5e0000 1.3e-002 -4.36 0.0 129 491 175 514 0.26273 5.3e-005 245 3 M0905_1.02 (HOXA4)_(Mus_musculus)_(DBD_1.00) NTAATKRNN 4.5e0000 6.1e-003 -5.10 0.0 72 492 103 477 0.14634 2.5e-005 245 3 M1007_1.02 (HOXA11)_(Mus_musculus)_(DBD_1.00) TTWAYKDBN 3.6e-003 4.9e-006 -12.22 0.0 254 492 191 281 0.51626 2.0e-008 245 3 M1012_1.02 (HOXB4)_(Mus_musculus)_(DBD_1.00) NTAATKRNN 3.2e0000 4.4e-003 -5.43 0.0 10 492 26 488 0.02033 1.8e-005 245 3 M1025_1.02 (HOXD1)_(Mus_musculus)_(DBD_0.98) NNYVATYA 9.1e0000 1.2e-002 -4.40 0.0 117 493 138 431 0.23732 5.0e-005 246 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 9.5e0000 1.3e-002 -4.36 0.0 61 491 95 517 0.12424 5.3e-005 245 3 M1163_1.02 (NKX6-3)_(PBM_CONSTRUCTS)_(DBD_1.00) NWTAATKRN 6.1e0000 8.2e-003 -4.80 0.0 70 492 102 487 0.14228 3.4e-005 245 3 M1863_1.02 FOXD1 GTAAACAW 4.8e-001 6.4e-004 -7.35 0.0 105 493 147 486 0.21298 2.6e-006 246 3 M2278_1.02 FOS DVTGASTCATB 1.0e-006 1.4e-009 -20.40 0.0 218 490 277 458 0.44490 5.6e-012 244 3 M2289_1.02 JUN DDRATGATGTMAT 1.8e-004 2.5e-007 -15.22 0.0 270 488 314 454 0.55328 1.0e-009 243 3 M2292_1.02 JUND DRTGASTCATS 3.2e-008 4.3e-011 -23.88 0.0 218 490 278 450 0.44490 1.7e-013 244 3 M2385_1.02 FOXP2 RWGTAAACAVR 3.4e-001 4.6e-004 -7.68 0.0 124 490 173 498 0.25306 1.9e-006 244 3 M4526_1.02 SMARCC1 DSRVDGTGASTCABV 1.3e-002 1.8e-005 -10.94 0.0 276 486 343 502 0.56790 7.3e-008 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 7.5e-007 1.0e-009 -20.71 0.0 221 487 277 450 0.45380 4.2e-012 243 3 M4567_1.02 FOXA2 NCWRWGTAAACANNN 3.9e-002 5.3e-005 -9.84 0.0 134 486 195 514 0.27572 2.2e-007 242 3 M4619_1.02 FOSL1 BGGTGASTCAK 3.1e-008 4.2e-011 -23.90 0.0 216 490 273 444 0.44082 1.7e-013 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 1.2e-006 1.6e-009 -20.26 0.0 220 486 279 456 0.45267 6.6e-012 242 3 M4629_1.02 NFE2 VRTGACTCAGCANWWYB 3.3e-003 4.4e-006 -12.33 0.0 152 484 183 412 0.31405 1.8e-008 241 3 M4681_1.02 BACH2 TGCTGAGTCA 2.3e-001 3.1e-004 -8.09 0.0 263 491 289 446 0.53564 1.3e-006 245 3 M5234_1.02 (SIM1)_(Drosophila_melanogaster)_(DBD_0.89) GGTCACGTAC 6.6e0000 8.8e-003 -4.73 0.0 373 491 320 379 0.75967 3.6e-005 245 3 M5292_1.02 ATF4 GKATGAYGCAATM 3.4e-003 4.6e-006 -12.29 0.0 268 488 288 422 0.54918 1.9e-008 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 8.2e-008 1.1e-010 -22.93 0.0 223 487 198 297 0.45791 4.5e-013 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.3e-007 1.8e-010 -22.45 0.0 211 487 117 165 0.43326 7.3e-013 243 3 M5310_1.02 BSX BTAATBRS 3.4e0000 4.5e-003 -5.40 0.0 115 493 156 494 0.23327 1.8e-005 246 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 5.1e-002 6.9e-005 -9.58 0.0 243 487 199 311 0.49897 2.9e-007 243 3 M5342_1.02 DLX4 NTAATTRB 5.1e-001 6.9e-004 -7.28 0.0 99 493 145 506 0.20081 2.8e-006 246 3 M5344_1.02 DLX6 NTAATTRB 2.3e0000 3.1e-003 -5.77 0.0 7 493 21 505 0.01420 1.3e-005 246 3 M5349_1.02 DUXA NTRAYYTAATCAN 5.3e0000 7.2e-003 -4.93 0.0 224 488 261 472 0.45902 3.0e-005 243 3 M5388_1.02 EMX2 VYTAATTAVB 8.1e0000 1.1e-002 -4.52 0.0 293 491 315 459 0.59674 4.5e-005 245 3 M5390_1.02 EN1 VBTAATTRSB 1.3e-001 1.8e-004 -8.62 0.0 7 491 23 499 0.01426 7.3e-007 245 3 M5394_1.02 EN2 NNTAATTRVN 9.2e0000 1.2e-002 -4.39 0.0 7 491 20 492 0.01426 5.1e-005 245 3 M5414_1.02 ESX1 SNTAATTRRN 1.4e0000 1.9e-003 -6.28 0.0 7 491 22 515 0.01426 7.6e-006 245 3 M5446_1.02 FOXD4L2 GTAAACA 1.8e-001 2.4e-004 -8.34 0.0 176 494 249 546 0.35628 9.7e-007 246 3 M5460_1.02 FOXL1 RTAAACA 2.4e-004 3.2e-007 -14.96 0.0 160 494 233 518 0.32389 1.3e-009 246 3 M5480_1.02 GBX1 RSTAATTRGB 9.0e0000 1.2e-002 -4.42 0.0 167 491 198 463 0.34012 5.0e-005 245 3 M5503_1.02 GSX2 DYTAATKRVN 2.5e0000 3.4e-003 -5.69 0.0 7 491 21 503 0.01426 1.4e-005 245 3 M5547_1.02 HOXC11 DGTCRTWAAAH 5.7e0000 7.7e-003 -4.87 0.0 170 490 206 470 0.34694 3.2e-005 244 3 M5555_1.02 HOXD11 RTCGTAAAAH 4.1e-001 5.5e-004 -7.50 0.0 171 491 204 449 0.34827 2.3e-006 245 3 M5587_1.02 JDP2 ATGASTCAT 9.5e-008 1.3e-010 -22.78 0.0 270 492 308 429 0.54878 5.2e-013 245 3 M5623_1.02 MEOX1 VSTAATTANC 1.6e-004 2.1e-007 -15.38 0.0 249 491 315 490 0.50713 8.5e-010 245 3 M5624_1.02 MEOX2 NSTAATTAWN 9.3e0000 1.3e-002 -4.38 0.0 23 491 45 515 0.04684 5.2e-005 245 3 M5635_1.02 MNX1 TTTAATTRNH 3.8e0000 5.2e-003 -5.27 0.0 171 491 213 485 0.34827 2.1e-005 245 3 M5772_1.02 RAX2 BTAATTRR 8.5e-001 1.1e-003 -6.77 0.0 7 493 22 501 0.01420 4.7e-006 246 3 M5873_1.02 TBR1 AGGTGTGAAA 2.5e0000 3.4e-003 -5.70 0.0 7 491 22 535 0.01426 1.4e-005 245 3 M5945_1.02 VAX2 YTAATTAN 6.0e-001 8.0e-004 -7.13 0.0 5 493 18 493 0.01014 3.3e-006 246 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 1.1e-007 1.5e-010 -22.63 0.0 223 489 226 350 0.45603 6.1e-013 244 3 M6114_1.02 FOXA1 WAWGYAAAYA 1.4e-002 1.9e-005 -10.90 0.0 131 491 193 516 0.26680 7.6e-008 245 3 M6152_1.02 ATF1 VTGACGTCAV 8.4e-001 1.1e-003 -6.79 0.0 331 491 363 473 0.67413 4.6e-006 245 3 M6167_1.02 CDX1 HCATAAAD 3.3e0000 4.5e-003 -5.40 0.0 137 493 201 559 0.27789 1.8e-005 246 3 M6180_1.02 CREB1 RTGACGTMA 1.5e-002 2.0e-005 -10.80 0.0 258 492 353 555 0.52439 8.3e-008 245 3 M6181_1.02 CREM CRVTGACGTCA 2.1e-002 2.8e-005 -10.47 0.0 218 490 290 518 0.44490 1.2e-007 244 3 M6228_1.02 FOSB CTGACTCAYV 7.0e-003 9.4e-006 -11.58 0.0 219 491 308 549 0.44603 3.8e-008 245 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 9.9e0000 1.3e-002 -4.31 0.0 136 486 159 434 0.27984 5.6e-005 242 3 M6239_1.02 FOXF2 HWADGTAAACA 8.4e0000 1.1e-002 -4.48 0.0 140 490 179 486 0.28571 4.7e-005 244 3 M6256_1.02 GATA4 RSWGATAAV 5.5e0000 7.3e-003 -4.91 0.0 132 492 194 560 0.26829 3.0e-005 245 3 M6258_1.02 GATA6 NWGATAA 1.0e0000 1.4e-003 -6.59 0.0 108 494 160 532 0.21862 5.6e-006 246 3 M6277_1.02 HLF SKRTTACRYAAYC 2.2e-002 3.0e-005 -10.41 0.0 182 488 217 439 0.37295 1.2e-007 243 3 M6296_1.02 HOXB6 KKCATMAATCAWY 6.4e0000 8.6e-003 -4.76 0.0 108 488 114 363 0.22131 3.5e-005 243 3 M6297_1.02 HOXB7 MATYAATCAA 6.0e0000 8.0e-003 -4.83 0.0 115 491 133 412 0.23422 3.3e-005 245 3 M6333_1.02 MAFG MATGACT 4.7e-005 6.3e-008 -16.59 0.0 224 494 330 564 0.45344 2.5e-010 246 3 M6359_1.02 NFE2L1 NATGACD 1.3e-003 1.7e-006 -13.28 0.0 262 494 372 573 0.53036 6.9e-009 246 3 M6360_1.02 NFE2L2 VRTGACTCAGCA 2.3e0000 3.0e-003 -5.79 0.0 63 489 110 575 0.12883 1.2e-005 244 3 M6368_1.02 NFIL3 VKVMRTTACRTAAY 2.0e0000 2.7e-003 -5.92 0.0 265 487 263 405 0.54415 1.1e-005 243 3 M6376_1.02 NKX2-5 TYAAGTG 2.1e-001 2.8e-004 -8.18 0.0 198 494 289 579 0.40081 1.1e-006 246 3 M6415_1.02 PDX1 CTAATTACY 1.8e-001 2.5e-004 -8.30 0.0 240 492 277 462 0.48780 1.0e-006 245 3 M6440_1.02 PRRX2 YTAATTR 2.8e0000 3.7e-003 -5.59 0.0 22 494 44 493 0.04453 1.5e-005 246 ## # 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).