# 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 ACACACACACACACACACACACACACACAC MEME-1 ACACACACACACACACACACACACACACAC 1.8e-003 2.3e-006 -12.97 0.0 71 471 42 114 0.15074 1.0e-008 235 1 TGAGTCA MEME-3 TGAGTCA 3.2e-014 4.3e-017 -37.69 0.0 194 494 144 204 0.39271 1.7e-019 246 1 VATGAYSTCACC MEME-5 VATGAYSTCACC 1.9e-006 2.5e-009 -19.80 0.0 109 489 112 277 0.22290 1.0e-011 244 1 GTGTGYSTRTGTGYGTGTGHGT MEME-7 GTGTGYSTRTGTGYGTGTGHGT 4.9e0000 6.6e-003 -5.03 0.0 155 479 68 138 0.32359 2.8e-005 239 1 TTTATGAGSTSW MEME-8 TTTATGAGSTSW 4.9e-005 6.5e-008 -16.54 0.0 29 489 40 220 0.05930 2.7e-010 244 2 TGACKCA DREME-1 TGACTCA 4.7e-015 6.3e-018 -39.61 0.0 184 494 134 191 0.37247 2.5e-020 246 2 TGACNTCA DREME-2 TGACVTCA 8.6e-004 1.1e-006 -13.68 0.0 115 493 58 122 0.23327 4.7e-009 246 2 GATWA DREME-4 GATWA 5.9e-002 7.9e-005 -9.44 0.0 130 496 126 324 0.26210 3.2e-007 247 2 ATAAAY DREME-5 ATAAAY 9.3e-004 1.2e-006 -13.60 0.0 199 495 121 199 0.40202 5.0e-009 247 3 M0300_1.02 (ATF2)_(Mus_musculus)_(DBD_1.00) NRTKACGTMA 3.9e-010 5.2e-013 -28.29 0.0 111 491 198 523 0.22607 2.1e-015 245 3 M0432_1.02 (ZFP161)_(Mus_musculus)_(DBD_1.00) NNCGYGCHH 4.1e0000 5.5e-003 -5.20 0.0 312 492 252 341 0.63415 2.3e-005 245 3 M0718_1.02 FOXK1 NNRTMAACAH 1.8e0000 2.4e-003 -6.01 0.0 107 491 162 545 0.21792 1.0e-005 245 3 M0719_1.02 FOXG1 RTAAACAW 2.2e-002 3.0e-005 -10.42 0.0 161 493 183 405 0.32657 1.2e-007 246 3 M0737_1.02 (FOXB2)_(Mus_musculus)_(DBD_0.94) WRWGTAAAYA 1.9e0000 2.6e-003 -5.96 0.0 109 491 160 529 0.22200 1.1e-005 245 3 M0887_1.02 HOXA2 NNYRAYBDN 1.2e-001 1.6e-004 -8.76 0.0 234 492 121 184 0.47561 6.4e-007 245 3 M0892_1.02 EMX1 VYTAATKASB 2.0e-001 2.7e-004 -8.21 0.0 201 491 248 479 0.40937 1.1e-006 245 3 M0893_1.02 ZFHX2 NNTAATTANN 4.8e0000 6.4e-003 -5.05 0.0 119 491 150 457 0.24236 2.6e-005 245 3 M0894_1.02 LBX1 TTAATTAG 2.7e-003 3.6e-006 -12.53 0.0 137 493 179 447 0.27789 1.5e-008 246 3 M0896_1.02 VENTX TTAATTAG 1.5e-003 2.0e-006 -13.15 0.0 171 493 203 422 0.34686 7.9e-009 246 3 M0900_1.02 SHOX NTAATTRV 8.0e0000 1.1e-002 -4.54 0.0 127 493 161 475 0.25761 4.4e-005 246 3 M0905_1.02 (HOXA4)_(Mus_musculus)_(DBD_1.00) NTAATKRNN 1.0e0000 1.4e-003 -6.60 0.0 128 492 168 477 0.26016 5.6e-006 245 3 M0949_1.02 (AC012531.1)_(Mus_musculus)_(DBD_1.00) NTAATDR 1.8e-001 2.4e-004 -8.33 0.0 168 494 218 489 0.34008 9.8e-007 246 3 M0999_1.02 (NKX6-1)_(Mus_musculus)_(DBD_1.00) NWTAATKRN 5.9e-001 7.9e-004 -7.14 0.0 126 492 175 505 0.25610 3.2e-006 245 3 M1007_1.02 (HOXA11)_(Mus_musculus)_(DBD_1.00) TTWAYKDBN 1.2e-002 1.6e-005 -11.05 0.0 96 492 118 382 0.19512 6.5e-008 245 3 M1012_1.02 (HOXB4)_(Mus_musculus)_(DBD_1.00) NTAATKRNN 7.2e0000 9.6e-003 -4.65 0.0 128 492 167 488 0.26016 3.9e-005 245 3 M1025_1.02 (HOXD1)_(Mus_musculus)_(DBD_0.98) NNYVATYA 5.9e-001 7.9e-004 -7.14 0.0 193 493 230 463 0.39148 3.2e-006 246 3 M1027_1.02 (HOXA6)_(Mus_musculus)_(DBD_1.00) HTAATKRBN 1.2e-002 1.6e-005 -11.01 0.0 170 492 229 496 0.34553 6.7e-008 245 3 M1030_1.02 (NKX2-3)_(Mus_musculus)_(DBD_1.00) NVYACTTVD 7.8e0000 1.0e-002 -4.56 0.0 76 492 125 573 0.15447 4.3e-005 245 3 M1034_1.02 (DBX2)_(Mus_musculus)_(DBD_0.93) NHVATNA 3.7e-003 5.0e-006 -12.21 0.0 168 494 127 247 0.34008 2.0e-008 246 3 M1073_1.02 (HOXA3)_(Mus_musculus)_(DBD_1.00) HTAATKRNN 1.0e0000 1.4e-003 -6.59 0.0 242 492 297 503 0.49187 5.6e-006 245 3 M1157_1.02 (HOXB9)_(PBM_CONSTRUCTS)_(DBD_1.00) WTTWATKRBN 5.6e0000 7.5e-003 -4.89 0.0 93 491 134 511 0.18941 3.1e-005 245 3 M1163_1.02 (NKX6-3)_(PBM_CONSTRUCTS)_(DBD_1.00) NWTAATKRN 2.4e-001 3.1e-004 -8.06 0.0 126 492 176 500 0.25610 1.3e-006 245 3 M1545_1.02 GMEB1 NNNRCGTNN 3.1e-001 4.1e-004 -7.80 0.0 214 492 238 435 0.43496 1.7e-006 245 3 M1863_1.02 FOXD1 GTAAACAW 3.0e0000 4.0e-003 -5.53 0.0 61 493 94 493 0.12373 1.6e-005 246 3 M2270_1.02 DUX4 TAAYYYAATCA 1.6e0000 2.2e-003 -6.14 0.0 158 490 174 410 0.32245 8.9e-006 244 3 M2278_1.02 FOS DVTGASTCATB 6.8e-005 9.0e-008 -16.22 0.0 194 490 249 463 0.39592 3.7e-010 244 3 M2289_1.02 JUN DDRATGATGTMAT 6.2e-007 8.3e-010 -20.90 0.0 88 488 140 442 0.18033 3.4e-012 243 3 M2292_1.02 JUND DRTGASTCATS 4.4e-011 5.9e-014 -30.46 0.0 290 490 343 442 0.59184 2.4e-016 244 3 M4526_1.02 SMARCC1 DSRVDGTGASTCABV 7.9e-005 1.1e-007 -16.07 0.0 260 486 330 491 0.53498 4.3e-010 242 3 M4565_1.02 FOSL2 VDGGATGASTCAYH 6.1e-009 8.2e-012 -25.53 0.0 211 487 281 463 0.43326 3.4e-014 243 3 M4567_1.02 FOXA2 VCWRWGTAAACANNN 9.7e-003 1.3e-005 -11.25 0.0 186 486 252 504 0.38272 5.4e-008 242 3 M4619_1.02 FOSL1 BGGTGASTCAK 2.6e-006 3.5e-009 -19.46 0.0 192 490 246 449 0.39184 1.5e-011 244 3 M4623_1.02 JUNB NDRTGASTCATNYHY 5.1e-007 6.8e-010 -21.11 0.0 292 486 350 465 0.60082 2.8e-012 242 3 M4629_1.02 NFE2 VRTGACTCAGCANWWYB 1.9e0000 2.5e-003 -5.97 0.0 100 484 116 389 0.20661 1.1e-005 241 3 M4681_1.02 BACH2 TGCTGAGTCA 3.9e-002 5.3e-005 -9.85 0.0 323 491 327 424 0.65784 2.1e-007 245 3 M5284_1.02 ALX3 BBTAATTRGY 8.0e-001 1.1e-003 -6.84 0.0 179 491 215 460 0.36456 4.4e-006 245 3 M5292_1.02 ATF4 GKATGAYGCAATM 4.4e-003 5.9e-006 -12.04 0.0 118 488 149 408 0.24180 2.4e-008 243 3 M5293_1.02 ATF7 NKATGACGTCATHN 6.2e-010 8.3e-013 -27.82 0.0 117 487 118 252 0.24025 3.4e-015 243 3 M5302_1.02 BATF3 TGATGACGTCATCA 1.1e-007 1.5e-010 -22.61 0.0 153 487 84 136 0.31417 6.3e-013 243 3 M5310_1.02 BSX BTAATBRS 4.5e-002 6.0e-005 -9.72 0.0 147 493 191 466 0.29817 2.4e-007 246 3 M5323_1.02 CREB3 KGRTGACGTCAYNV 1.8e-004 2.3e-007 -15.27 0.0 169 487 142 270 0.34702 9.6e-010 243 3 M5343_1.02 DLX5 NTAATTRN 1.2e-001 1.7e-004 -8.70 0.0 123 493 169 483 0.24949 6.8e-007 246 3 M5349_1.02 DUXA NTRAYBTAATCAN 2.8e-002 3.7e-005 -10.20 0.0 152 488 189 440 0.31148 1.5e-007 243 3 M5388_1.02 EMX2 VYTAATTAVB 5.0e-003 6.7e-006 -11.92 0.0 127 491 161 422 0.25866 2.7e-008 245 3 M5390_1.02 EN1 VBTAATTRSB 3.6e0000 4.8e-003 -5.33 0.0 127 491 164 477 0.25866 2.0e-005 245 3 M5414_1.02 ESX1 SNTAATTRRN 7.0e0000 9.4e-003 -4.67 0.0 83 491 117 488 0.16904 3.8e-005 245 3 M5428_1.02 EVX2 NBTAATKABB 2.2e0000 3.0e-003 -5.82 0.0 129 491 174 498 0.26273 1.2e-005 245 3 M5446_1.02 FOXD4L2 GTAAACA 9.3e-005 1.2e-007 -15.90 0.0 158 494 242 541 0.31984 5.0e-010 246 3 M5460_1.02 FOXL1 RTAAACA 5.0e-002 6.6e-005 -9.62 0.0 102 494 153 509 0.20648 2.7e-007 246 3 M5480_1.02 GBX1 RSTAATTRGB 1.5e0000 2.1e-003 -6.18 0.0 183 491 211 445 0.37271 8.5e-006 245 3 M5481_1.02 GBX2 NYTAATTRSB 1.2e0000 1.7e-003 -6.40 0.0 77 491 109 464 0.15682 6.8e-006 245 3 M5493_1.02 GMEB2 KTRCGTAA 5.1e-002 6.8e-005 -9.60 0.0 181 493 211 435 0.36714 2.7e-007 246 3 M5502_1.02 GSX1 NBTAATKRSN 7.9e-002 1.1e-004 -9.15 0.0 127 491 179 498 0.25866 4.3e-007 245 3 M5503_1.02 GSX2 DYTAATKRSN 4.3e-001 5.8e-004 -7.46 0.0 127 491 173 490 0.25866 2.4e-006 245 3 M5519_1.02 HMX2 NDTTAAKTGBT 1.3e0000 1.7e-003 -6.38 0.0 120 490 170 513 0.24490 6.9e-006 244 3 M5520_1.02 HMX3 BNTTAAKTGNY 4.1e-001 5.5e-004 -7.51 0.0 112 490 166 523 0.22857 2.3e-006 244 3 M5541_1.02 HOXB2 NNTAATKANN 6.1e-001 8.1e-004 -7.12 0.0 125 491 170 491 0.25458 3.3e-006 245 3 M5542_1.02 HOXB3 NYTAATKRNN 2.8e-001 3.8e-004 -7.88 0.0 129 491 173 480 0.26273 1.6e-006 245 3 M5544_1.02 HOXC10 DTTTWATKGB 2.6e0000 3.5e-003 -5.65 0.0 17 491 38 505 0.03462 1.4e-005 245 3 M5547_1.02 HOXC11 DGTCRTWAAAH 2.6e-003 3.5e-006 -12.56 0.0 100 490 146 465 0.20408 1.4e-008 244 3 M5555_1.02 HOXD11 RTCGTAAAAH 6.9e-002 9.2e-005 -9.30 0.0 91 491 124 437 0.18534 3.7e-007 245 3 M5583_1.02 ISL2 YTAAKTGC 1.9e0000 2.6e-003 -5.96 0.0 55 493 94 543 0.11156 1.1e-005 246 3 M5587_1.02 JDP2 ATGASTCAT 1.0e-008 1.3e-011 -25.03 0.0 182 492 224 406 0.36992 5.5e-014 245 3 M5602_1.02 LHX9 YTAATTRN 1.7e0000 2.3e-003 -6.08 0.0 117 493 157 484 0.23732 9.3e-006 246 3 M5604_1.02 LMX1A YTAATTAA 2.0e0000 2.7e-003 -5.92 0.0 179 493 200 431 0.36308 1.1e-005 246 3 M5605_1.02 LMX1B TTAATTRN 9.0e0000 1.2e-002 -4.42 0.0 131 493 165 476 0.26572 4.9e-005 246 3 M5623_1.02 MEOX1 VSTAATTANS 9.6e-005 1.3e-007 -15.87 0.0 149 491 202 459 0.30346 5.3e-010 245 3 M5624_1.02 MEOX2 NSTAATTAWN 1.6e-003 2.1e-006 -13.07 0.0 171 491 231 487 0.34827 8.6e-009 245 3 M5631_1.02 MIXL1 NBTAATTRVN 1.5e0000 2.0e-003 -6.22 0.0 127 491 165 472 0.25866 8.1e-006 245 3 M5632_1.02 MLX RTCACGTGAT 2.1e0000 2.8e-003 -5.87 0.0 139 491 131 333 0.28310 1.2e-005 245 3 M5635_1.02 MNX1 KTTAATTRNH 2.6e-004 3.5e-007 -14.86 0.0 127 491 183 478 0.25866 1.4e-009 245 3 M5702_1.02 PAX1 DKCABTCAWGCGTGACG 7.0e0000 9.3e-003 -4.68 0.0 76 484 60 228 0.15702 3.9e-005 241 3 M5715_1.02 PHOX2B TAATBYAATTA 7.4e0000 9.9e-003 -4.62 0.0 98 490 117 414 0.20000 4.1e-005 244 3 M5746_1.02 POU6F2 WTAATKAGST 4.9e0000 6.6e-003 -5.03 0.0 123 491 151 448 0.25051 2.7e-005 245 3 M5772_1.02 RAX2 BTAATTRR 2.0e0000 2.7e-003 -5.93 0.0 127 493 166 479 0.25761 1.1e-005 246 3 M5807_1.02 SHOX2 YTAATTRR 9.6e0000 1.3e-002 -4.36 0.0 127 493 157 463 0.25761 5.2e-005 246 3 M5941_1.02 UNCX NTAATYBAATTAN 6.0e-001 8.1e-004 -7.12 0.0 66 488 98 460 0.13525 3.3e-006 243 3 M5944_1.02 VAX1 YTAATTAN 1.5e0000 2.0e-003 -6.23 0.0 179 493 224 488 0.36308 8.0e-006 246 3 M5945_1.02 VAX2 YTAATTAB 4.2e-002 5.6e-005 -9.79 0.0 221 493 273 485 0.44828 2.3e-007 246 3 M5998_1.02 (CREB5)_(Mus_musculus)_(DBD_1.00) DRTGACGTCATN 2.8e-010 3.8e-013 -28.61 0.0 169 489 177 312 0.34560 1.5e-015 244 3 M6114_1.02 FOXA1 WAWGYAAAYA 2.9e-003 3.9e-006 -12.46 0.0 185 491 252 504 0.37678 1.6e-008 245 3 M6151_1.02 ARNT BYRCGTGC 4.7e-001 6.2e-004 -7.38 0.0 165 493 198 450 0.33469 2.5e-006 246 3 M6152_1.02 ATF1 VTGACGTCAV 6.9e-001 9.2e-004 -6.99 0.0 155 491 192 461 0.31568 3.8e-006 245 3 M6180_1.02 CREB1 RTGACGTMA 7.8e-002 1.0e-004 -9.17 0.0 152 492 217 527 0.30894 4.2e-007 245 3 M6181_1.02 CREM CRVTGACGTCA 5.6e-001 7.5e-004 -7.20 0.0 172 490 221 491 0.35102 3.1e-006 244 3 M6197_1.02 E4F1 YGTKACGTC 9.3e-004 1.2e-006 -13.60 0.0 192 492 234 445 0.39024 5.0e-009 245 3 M6228_1.02 FOSB CTGACTCAYV 2.6e-003 3.5e-006 -12.58 0.0 117 491 188 545 0.23829 1.4e-008 245 3 M6234_1.02 FOXA3 RVWAARYAAAYAD 4.3e-001 5.7e-004 -7.47 0.0 184 488 238 496 0.37705 2.4e-006 243 3 M6235_1.02 FOXC1 CYWAAGTAAACAWHG 3.3e-001 4.5e-004 -7.71 0.0 162 486 183 411 0.33333 1.8e-006 242 3 M6239_1.02 FOXF2 HWADGTAAACA 9.9e-003 1.3e-005 -11.23 0.0 116 490 165 477 0.23673 5.5e-008 244 3 M6275_1.02 HIF1A SBSTACGTGCSB 2.1e0000 2.8e-003 -5.88 0.0 215 489 244 451 0.43967 1.1e-005 244 3 M6277_1.02 HLF SKRTTACRYAAYC 4.4e-003 5.9e-006 -12.03 0.0 118 488 144 392 0.24180 2.4e-008 243 3 M6289_1.02 HOXA9 WCATAAAYYRTM 1.1e0000 1.5e-003 -6.50 0.0 163 489 195 451 0.33333 6.2e-006 244 3 M6290_1.02 HOXA13 CCAATAAWAHC 1.4e0000 1.8e-003 -6.31 0.0 124 490 166 484 0.25306 7.5e-006 244 3 M6292_1.02 HOXA5 CATTAATYAR 1.0e0000 1.3e-003 -6.62 0.0 201 491 225 437 0.40937 5.5e-006 245 3 M6296_1.02 HOXB6 KKCATMAATCAWY 3.7e-001 5.0e-004 -7.61 0.0 268 488 227 336 0.54918 2.0e-006 243 3 M6297_1.02 HOXB7 MATYAATCAA 1.2e0000 1.6e-003 -6.44 0.0 173 491 183 398 0.35234 6.5e-006 245 3 M6298_1.02 HOXB8 BMATTAATCAA 8.8e-001 1.2e-003 -6.75 0.0 208 490 198 366 0.42449 4.8e-006 244 3 M6315_1.02 ISL1 SYTAATR 1.5e0000 2.0e-003 -6.22 0.0 190 494 236 490 0.38462 8.1e-006 246 3 M6326_1.02 KLF8 CAGGGKGTG 8.2e0000 1.1e-002 -4.52 0.0 316 492 398 551 0.64228 4.5e-005 245 3 M6333_1.02 MAFG MATGACT 7.4e-008 9.9e-011 -23.04 0.0 80 494 159 564 0.16194 4.0e-013 246 3 M6359_1.02 NFE2L1 NATGACD 6.0e-009 8.0e-012 -25.56 0.0 206 494 326 568 0.41700 3.2e-014 246 3 M6368_1.02 NFIL3 VKVMVTTACRTAAY 1.4e-002 1.8e-005 -10.91 0.0 113 487 121 334 0.23203 7.5e-008 243 3 M6380_1.02 NOBOX HTAATTRSY 4.8e-001 6.5e-004 -7.34 0.0 78 492 111 459 0.15854 2.6e-006 245 3 M6406_1.02 PAX2 RHKCAGTSAYGMGTGAYW 1.1e-001 1.5e-004 -8.81 0.0 85 483 131 497 0.17598 6.2e-007 241 3 M6415_1.02 PDX1 CTAATTACY 2.0e-002 2.7e-005 -10.51 0.0 232 492 261 437 0.47154 1.1e-007 245 3 M6427_1.02 POU4F2 MARCTCATTAATR 3.2e0000 4.3e-003 -5.46 0.0 72 488 91 404 0.14754 1.8e-005 243 3 M6473_1.02 SOX17 CAMMAATNHHCATTGTCS 3.4e0000 4.5e-003 -5.40 0.0 71 483 70 289 0.14700 1.9e-005 241 3 M6506_1.02 TCF7 VHSCTTTGWWST 5.1e0000 6.8e-003 -5.00 0.0 25 489 51 547 0.05112 2.8e-005 244 3 M6510_1.02 TEF TGTTTATRTAAMTK 3.3e0000 4.5e-003 -5.41 0.0 165 487 209 485 0.33881 1.8e-005 243 ## # 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).