# 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 CASTCAMRYWSACACA MEME-1 CASTCAMRYWSACACA 1.6e-069 2.2e-072 -165.00 0.0 81 485 211 351 0.16701 9.1e-075 242 1 TGTTTDACCARMTATCTGGGCAYCCYDTRGC MEME-2 TGTTTDACCARMTATCTGGGCAYCCYDTRGC 1.2e-076 1.6e-079 -181.44 0.0 116 470 159 170 0.24681 6.8e-082 234 1 TAAAATTAACCATCAC MEME-3 TAAAATTAACCATCAC 2.5e-042 3.4e-045 -102.39 0.0 107 485 144 208 0.22062 1.4e-047 242 2 TCTGGGYA DREME-1 TCTGGGCA 4.0e-064 5.4e-067 -152.59 0.0 71 493 132 183 0.14402 2.2e-069 246 2 AASTTGAC DREME-2 AASTTGAC 2.0e-063 2.7e-066 -150.99 0.0 97 493 122 137 0.19675 1.1e-068 246 2 AAMATTA DREME-3 AAMATTA 7.1e-016 9.5e-019 -41.49 0.0 82 494 89 195 0.16599 3.9e-021 246 2 TGGGCYA DREME-4 TGGGCCA 4.9e-039 6.5e-042 -94.83 0.0 48 494 92 180 0.09717 2.7e-044 246 2 TTCTGGR DREME-5 TTCTGGG 2.8e-015 3.8e-018 -40.11 0.0 138 494 126 216 0.27935 1.5e-020 246 2 MCCAGCTA DREME-6 ACCAGCTA 3.3e-005 4.4e-008 -16.93 0.0 89 493 49 109 0.18053 1.8e-010 246 2 CMTCACAG DREME-7 CMTCACAG 4.1e-013 5.5e-016 -35.14 0.0 137 493 73 107 0.27789 2.2e-018 246 2 ACCAAATA DREME-8 ACCAAATA 1.3e-011 1.7e-014 -31.69 0.0 111 493 103 211 0.22515 7.0e-017 246 2 ACATRAAA DREME-9 ACATAAAA 3.7e-013 4.9e-016 -35.24 0.0 85 493 112 288 0.17241 2.0e-018 246 2 CTGGGC DREME-10 CTGGGC 5.1e-036 6.9e-039 -87.88 0.0 67 495 164 404 0.13535 2.8e-041 247 3 M0108_1.02 (ARID5A)_(Mus_musculus)_(DBD_0.97) NNTAATATTKN 8.2e-001 1.1e-003 -6.81 0.0 86 490 112 424 0.17551 4.5e-006 244 3 M0199_1.02 (HES2)_(Mus_musculus)_(DBD_0.83) NNNNGRCACGTGM 2.4e-002 3.2e-005 -10.33 0.0 56 488 108 567 0.11475 1.3e-007 243 3 M0214_1.02 (TCF21)_(Mus_musculus)_(DBD_1.00) AACAKMTGK 1.2e-002 1.7e-005 -11.01 0.0 72 492 110 457 0.14634 6.7e-008 245 3 M0405_1.02 (KLF7)_(Mus_musculus)_(DBD_1.00) DGGGCGKGGY 4.3e0000 5.8e-003 -5.15 0.0 211 491 298 580 0.42974 2.4e-005 245 3 M0443_1.02 (KLF12)_(Mus_musculus)_(DBD_1.00) DGGGYGKGKY 2.3e-001 3.1e-004 -8.08 0.0 127 491 203 584 0.25866 1.3e-006 245 3 M0629_1.02 DMRT3 MATGTATCAAN 3.0e-001 4.0e-004 -7.83 0.0 76 490 117 496 0.15510 1.6e-006 244 3 M0630_1.02 DMRT1 WWTGTWDCNW 5.7e0000 7.6e-003 -4.88 0.0 65 491 103 529 0.13238 3.1e-005 245 3 M0632_1.02 DMRTA2 HHWGTWDYNN 5.0e-005 6.7e-008 -16.51 0.0 71 491 90 322 0.14460 2.7e-010 245 3 M0633_1.02 DMRT2 KAATKTATWN 2.1e0000 2.9e-003 -5.86 0.0 93 491 125 461 0.18941 1.2e-005 245 3 M0897_1.02 HOXB13 DTTWAYDRBN 1.8e-003 2.4e-006 -12.95 0.0 75 491 127 509 0.15275 9.7e-009 245 3 M0901_1.02 AC226150.2 CWTGTCAA 7.2e0000 9.7e-003 -4.64 0.0 83 493 131 559 0.16836 3.9e-005 246 3 M0999_1.02 (NKX6-1)_(Mus_musculus)_(DBD_1.00) NWTAATKRN 5.8e0000 7.7e-003 -4.87 0.0 104 492 144 501 0.21138 3.2e-005 245 3 M1007_1.02 (HOXA11)_(Mus_musculus)_(DBD_1.00) TTWAYKDBN 1.2e-001 1.6e-004 -8.74 0.0 72 492 65 242 0.14634 6.5e-007 245 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 7.8e-001 1.0e-003 -6.87 0.0 75 491 113 493 0.15275 4.3e-006 245 3 M1628_1.02 (TBX10)_(Mus_musculus)_(DBD_0.87) AGGTGTGAANN 6.0e-001 8.0e-004 -7.13 0.0 146 490 216 556 0.29796 3.3e-006 244 3 M1927_1.02 (MYCL1)_(Mus_musculus)_(DBD_0.66) RCCACGTG 2.5e0000 3.4e-003 -5.69 0.0 47 493 76 483 0.09533 1.4e-005 246 3 M1929_1.02 TP53 CATGTCTGGRCATGY 2.2e-004 2.9e-007 -15.05 0.0 120 486 149 387 0.24691 1.2e-009 242 3 M2321_1.02 TP63 NDRCAWGYHCARRCWTGYHY 1.2e-001 1.6e-004 -8.73 0.0 135 481 190 497 0.28067 6.7e-007 240 3 M4438_1.02 ESRRA RGGTCANKSTGACCY 1.8e0000 2.4e-003 -6.03 0.0 30 486 59 528 0.06173 9.9e-006 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 3.4e0000 4.6e-003 -5.38 0.0 31 487 52 447 0.06366 1.9e-005 243 3 M5234_1.02 (SIM1)_(Drosophila_melanogaster)_(DBD_0.89) GGTCACGTAC 1.2e-007 1.6e-010 -22.56 0.0 73 491 112 383 0.14868 6.5e-013 245 3 M5303_1.02 BCL6B TGCTTTCTAGGAATTCM 1.2e0000 1.6e-003 -6.44 0.0 66 484 25 73 0.13636 6.7e-006 241 3 M5339_1.02 DLX1 NNTAATTRNN 5.1e0000 6.9e-003 -4.98 0.0 79 491 114 489 0.16090 2.8e-005 245 3 M5344_1.02 DLX6 NTAATTRB 9.1e0000 1.2e-002 -4.40 0.0 103 493 144 508 0.20892 5.0e-005 246 3 M5512_1.02 HIC2 VSYGGGCAY 1.8e-014 2.5e-017 -38.24 0.0 80 492 184 587 0.16260 1.0e-019 245 3 M5544_1.02 HOXC10 DTTTWATKDB 5.9e-004 7.9e-007 -14.05 0.0 77 491 134 522 0.15682 3.2e-009 245 3 M5547_1.02 HOXC11 DGTCRTWAAAH 4.0e-001 5.4e-004 -7.53 0.0 74 490 107 459 0.15102 2.2e-006 244 3 M5605_1.02 LMX1B TTAATTRN 2.4e0000 3.2e-003 -5.75 0.0 77 493 113 493 0.15619 1.3e-005 246 3 M5621_1.02 MEIS3 SCTGTCAH 6.5e-005 8.7e-008 -16.26 0.0 75 493 146 580 0.15213 3.5e-010 246 3 M5628_1.02 MGA AGGTGTGA 1.1e0000 1.5e-003 -6.53 0.0 173 493 253 575 0.35091 5.9e-006 246 3 M5857_1.02 SPDEF AMCCGGATGTW 1.2e-005 1.6e-008 -17.98 0.0 106 490 145 405 0.21633 6.4e-011 244 3 M5873_1.02 TBR1 AGGTGTGAAA 3.4e-001 4.5e-004 -7.71 0.0 145 491 212 545 0.29532 1.8e-006 245 3 M5883_1.02 TBX20 TCACACSTTCACACCT 5.3e-008 7.1e-011 -23.37 0.0 93 485 136 392 0.19175 2.9e-013 242 3 M5896_1.02 TBX4 AGGTGTGA 5.8e-002 7.8e-005 -9.46 0.0 143 493 225 581 0.29006 3.2e-007 246 3 M5965_1.02 ZIC4 DCDCMGCRGGGGGYC 3.0e-002 4.1e-005 -10.11 0.0 50 486 91 507 0.10288 1.7e-007 242 3 M5977_1.02 ZNF740 GTGGGGGGGK 7.4e0000 9.9e-003 -4.61 0.0 269 491 339 535 0.54786 4.1e-005 245 3 M5981_1.02 ZSCAN4 TTTTCAGKGTGTGCA 3.5e-016 4.6e-019 -42.22 0.0 150 486 209 386 0.30864 1.9e-021 242 3 M6037_1.02 (IRX1)_(Mus_musculus)_(DBD_1.00) TTTKTCATGTWR 5.7e-001 7.6e-004 -7.19 0.0 87 489 121 458 0.17791 3.1e-006 244 3 M6115_1.02 TP73 CATGYCWGRRCHTGY 5.0e-003 6.7e-006 -11.92 0.0 118 486 187 538 0.24280 2.7e-008 242 3 M6167_1.02 CDX1 HCATAAAD 1.4e-005 1.9e-008 -17.79 0.0 83 493 153 551 0.16836 7.6e-011 246 3 M6199_1.02 EGR2 DGVGTGGGCGG 7.8e-001 1.1e-003 -6.86 0.0 270 490 354 549 0.55102 4.3e-006 244 3 M6200_1.02 EGR3 WGAGTGGGYGT 2.0e-008 2.7e-011 -24.34 0.0 272 490 393 555 0.55510 1.1e-013 244 3 M6212_1.02 EPAS1 CMCACGYAYDCAC 6.5e-003 8.7e-006 -11.65 0.0 152 488 228 539 0.31148 3.6e-008 243 3 M6266_1.02 GLI3 BTGGGTGGTCY 2.8e-001 3.8e-004 -7.88 0.0 270 490 351 540 0.55102 1.5e-006 244 3 M6272_1.02 HESX1 AKKYYAYKWGCCRSVT 6.5e-005 8.7e-008 -16.26 0.0 73 485 138 545 0.15052 3.6e-010 242 3 M6274_1.02 HIC1 GGGKTGCCC 7.1e-020 9.5e-023 -50.71 0.0 88 492 202 555 0.17886 3.9e-025 245 3 M6289_1.02 HOXA9 WCATAAAYYRTH 1.2e0000 1.5e-003 -6.47 0.0 83 489 118 471 0.16973 6.3e-006 244 3 M6290_1.02 HOXA13 CCAATAAWAHC 8.9e-003 1.2e-005 -11.34 0.0 62 490 107 503 0.12653 4.9e-008 244 3 M6297_1.02 HOXB7 MATYAATCAA 9.4e-001 1.3e-003 -6.67 0.0 97 491 116 398 0.19756 5.2e-006 245 3 M6303_1.02 HOXD4 TTAATTKW 1.5e0000 2.0e-003 -6.22 0.0 79 493 120 512 0.16024 8.1e-006 246 3 M6304_1.02 HOXD9 HMATNAAWYT 8.4e-007 1.1e-009 -20.60 0.0 87 491 149 487 0.17719 4.6e-012 245 3 M6323_1.02 KLF3 HRCYWGGGTGKGGCT 1.0e-003 1.3e-006 -13.52 0.0 288 486 384 539 0.59259 5.5e-009 242 3 M6326_1.02 KLF8 CAGGGKGTG 7.3e-009 9.8e-012 -25.35 0.0 90 492 174 550 0.18293 4.0e-014 245 3 M6347_1.02 MSX2 TAATTNK 6.0e-001 8.1e-004 -7.12 0.0 118 494 167 510 0.23887 3.3e-006 246 3 M6385_1.02 NR1I2 VTGAMCTYNNTTRACCYHH 1.2e-013 1.6e-016 -36.39 0.0 68 482 151 517 0.14108 6.5e-019 240 3 M6387_1.02 NR1I3 HTGAACTYBBYTGACCYY 4.6e-004 6.1e-007 -14.31 0.0 37 483 77 493 0.07660 2.5e-009 241 3 M6411_1.02 PAX8 BTVAYTSRMGYRKR 3.5e0000 4.7e-003 -5.35 0.0 27 487 58 580 0.05544 2.0e-005 243 3 M6415_1.02 PDX1 CTAATTACY 4.8e0000 6.5e-003 -5.04 0.0 458 492 415 425 0.93089 2.7e-005 245 3 M6416_1.02 CBFB YYTGTGGTYDB 3.3e-003 4.5e-006 -12.32 0.0 142 490 232 585 0.28980 1.8e-008 244 3 M6419_1.02 PKNOX1 MATCARTCAABYB 3.0e-001 4.0e-004 -7.82 0.0 68 488 113 525 0.13934 1.7e-006 243 3 M6422_1.02 PLAGL1 CRGGGGGCCC 6.9e-001 9.3e-004 -6.98 0.0 43 491 77 521 0.08758 3.8e-006 245 3 M6429_1.02 POU6F1 CATAAWTTATGCR 1.7e0000 2.3e-003 -6.09 0.0 110 488 89 260 0.22541 9.3e-006 243 3 M6451_1.02 RFX1 GTTGCYAGGSRA 5.8e-001 7.7e-004 -7.16 0.0 89 489 139 531 0.18200 3.2e-006 244 3 M6456_1.02 RREB1 DKGKKKGKGGKTGKTTKGGGKT 2.1e-005 2.9e-008 -17.36 0.0 167 479 244 501 0.34864 1.2e-010 239 3 M6459_1.02 RUNX3 AACCRCAAAMCCCV 2.0e0000 2.7e-003 -5.90 0.0 259 487 310 494 0.53183 1.1e-005 243 3 M6516_1.02 TCF3 RRVCATCTGKT 7.0e-001 9.3e-004 -6.98 0.0 28 490 61 571 0.05714 3.8e-006 244 3 M6519_1.02 TGIF1 MWGSTGACACCTSMCA 1.1e-003 1.5e-006 -13.42 0.0 77 485 146 579 0.15876 6.1e-009 242 3 M6525_1.02 TLX1 YGBYAAKDWGS 3.7e-003 5.0e-006 -12.22 0.0 42 490 91 577 0.08571 2.0e-008 244 3 M6529_1.02 UBP1 TYTCTGS 9.8e-003 1.3e-005 -11.24 0.0 140 494 226 584 0.28340 5.3e-008 246 3 M6546_1.02 ZFHX3 ATTAWTAATTA 5.3e-003 7.1e-006 -11.85 0.0 88 490 109 368 0.17959 2.9e-008 244 3 M6554_1.02 ZNF238 TCCAGATGTTBVSS 1.4e-007 1.9e-010 -22.41 0.0 143 487 194 424 0.29363 7.6e-013 243 3 M6558_1.02 ZNF423 GCACCCTWGGGTGYC 7.6e-001 1.0e-003 -6.88 0.0 100 486 44 113 0.20576 4.2e-006 242 ## # 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).