******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) For further information on how to interpret these results please access https://meme-suite.org/meme. To get a copy of the MEME Suite software please access https://meme-suite.org. ******************************************************************************** ******************************************************************************** REFERENCE ******************************************************************************** If you use this program in your research, please cite: Timothy L. Bailey and Charles Elkan, "Fitting a mixture model by expectation maximization to discover motifs in biopolymers", Proceedings of the Second International Conference on Intelligent Systems for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994. ******************************************************************************** ******************************************************************************** TRAINING SET ******************************************************************************** PRIMARY SEQUENCES= /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/seqs-centered CONTROL SEQUENCES= --none-- ALPHABET= ACGT ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/seqs-centered -oc /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/meme_out -mod zoops -nmotifs 10 -minw 6 -maxw 15 -bfile /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/background -dna -revcomp -nostatus model: mod= zoops nmotifs= 10 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 6 maxw= 15 nsites: minsites= 2 maxsites= 14321 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 1432100 N= 14321 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.191 C 0.309 G 0.309 T 0.191 Background letter frequencies (from file /scratch/jngalang/MotifAnalysis/NewMemeChip/GRCh38-107_AZ_exp1_d0_TRIM1_1_peaks/background): A 0.188 C 0.312 G 0.312 T 0.188 Background model order: 2 ******************************************************************************** ******************************************************************************** MOTIF AAAAAWAMAAAAAWW MEME-1 width = 15 sites = 1600 llr = 21574 E-value = 3.5e-269 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAWAMAAAAAWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 889984749898744 pos.-specific C 11:::114:1:1111 probability G :1::1:11:::1:1: matrix T 11111511:11:145 bits 2.4 2.2 1.9 * * * 1.7 ** * * Relative 1.4 *** * ** Entropy 1.2 ***** ***** (19.5 bits) 1.0 ******* ***** * 0.7 ******* ******* 0.5 ******* ******* 0.2 *************** 0.0 --------------- Multilevel AAAAATACAAAAATT consensus A A AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAWAMAAAAAWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 11.8532 E= 3.5e-269 203 -218 -318 -56 205 -192 -234 -124 222 -796 -392 -87 226 -738 -596 -98 213 -638 -218 -80 115 -209 -1729 144 195 -224 -180 -68 95 47 -171 -76 233 -738 -306 -342 205 -138 -664 -94 231 -1729 -896 -145 213 -174 -190 -665 196 -131 -638 -42 105 -254 -146 124 120 -238 -301 133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAWAMAAAAAWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1600 E= 3.5e-269 0.769375 0.068750 0.034375 0.127500 0.776250 0.082500 0.061875 0.079375 0.875625 0.001250 0.020625 0.102500 0.898125 0.001875 0.005000 0.095000 0.820000 0.003750 0.068750 0.107500 0.415625 0.073125 0.000000 0.511250 0.727500 0.066250 0.089375 0.116875 0.361875 0.431250 0.095625 0.111250 0.943125 0.001875 0.037500 0.017500 0.778750 0.120000 0.003125 0.098125 0.930625 0.000000 0.000625 0.068750 0.820625 0.093750 0.083750 0.001875 0.730000 0.126250 0.003750 0.140000 0.388750 0.053750 0.113125 0.444375 0.430000 0.060000 0.038750 0.471250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAWAMAAAAAWW MEME-1 regular expression -------------------------------------------------------------------------------- AAAAA[TA]A[CA]AAAAA[TA][TA] -------------------------------------------------------------------------------- Time 305.92 secs. ******************************************************************************** ******************************************************************************** MOTIF RKWGCTGGGATTACA MEME-2 width = 15 sites = 751 llr = 11865 E-value = 8.6e-135 ******************************************************************************** -------------------------------------------------------------------------------- Motif RKWGCTGGGATTACA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 515:::111a::9:a pos.-specific C ::::9:::::21:9: probability G 55:9::999:::::: matrix T :55:1a::::79:1: bits 2.4 * 2.2 * * * 1.9 * * ** * 1.7 * * ** * Relative 1.4 * * ** ** * Entropy 1.2 *********** * (22.8 bits) 1.0 * ************* 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGTGCTGGGATTACA consensus GTA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RKWGCTGGGATTACA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 12.7741 E= 8.6e-135 149 -507 57 -714 -185 -348 56 129 140 -587 -1620 141 -268 -407 158 -323 -382 156 -487 -171 -1620 -429 -787 239 -139 -787 154 -323 -153 -555 157 -714 -175 -687 159 -714 241 -1620 -687 -1620 -397 -41 -587 199 -1620 -245 -687 232 234 -455 -307 -1620 -333 150 -417 -116 239 -787 -687 -397 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RKWGCTGGGATTACA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 751 E= 8.6e-135 0.527297 0.009321 0.462051 0.001332 0.051931 0.027963 0.460719 0.459387 0.494008 0.005326 0.000000 0.500666 0.029294 0.018642 0.932091 0.019973 0.013316 0.918775 0.010652 0.057257 0.000000 0.015979 0.001332 0.982690 0.071904 0.001332 0.906791 0.019973 0.065246 0.006658 0.926764 0.001332 0.055925 0.002663 0.940080 0.001332 0.997337 0.000000 0.002663 0.000000 0.011984 0.234354 0.005326 0.748336 0.000000 0.057257 0.002663 0.940080 0.949401 0.013316 0.037284 0.000000 0.018642 0.880160 0.017310 0.083888 0.984021 0.001332 0.002663 0.011984 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RKWGCTGGGATTACA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][GT][TA]GCTGGGA[TC]TACA -------------------------------------------------------------------------------- Time 549.76 secs. ******************************************************************************** ******************************************************************************** MOTIF TGTTGSCCAGGCTGG MEME-3 width = 15 sites = 670 llr = 10237 E-value = 1.0e-113 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTTGSCCAGGCTGG MEME-3 Description -------------------------------------------------------------------------------- Simplified A :1::2:::a::1::: pos.-specific C :::2:599:::9::: probability G :9::84:::9a::a9 matrix T 9:a8::1:::::a:: bits 2.4 * * 2.2 * * * 1.9 * * * * 1.7 * * * * * Relative 1.4 * * *** ** Entropy 1.2 **** ********* (22.0 bits) 1.0 ***** ********* 0.7 ***** ********* 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TGTTGCCCAGGCTGG consensus CAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTGSCCAGGCTGG MEME-3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 12.699 E= 1.0e-113 -397 -306 -770 234 -133 -1603 153 -281 -439 -1603 -1603 240 -397 -53 -401 200 9 -1603 134 -397 -252 68 47 -239 -697 148 -439 -71 -381 159 -571 -217 238 -539 -454 -1603 -212 -1603 159 -352 -539 -1603 167 -1603 -95 149 -1603 -273 -417 -1603 -1603 240 -222 -770 162 -697 -265 -390 158 -339 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTGSCCAGGCTGG MEME-3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 670 E= 1.0e-113 0.011940 0.037313 0.001493 0.949254 0.074627 0.000000 0.898507 0.026866 0.008955 0.000000 0.000000 0.991045 0.011940 0.216418 0.019403 0.752239 0.200000 0.000000 0.788060 0.011940 0.032836 0.500000 0.431343 0.035821 0.001493 0.868657 0.014925 0.114925 0.013433 0.938806 0.005970 0.041791 0.979104 0.007463 0.013433 0.000000 0.043284 0.000000 0.940299 0.016418 0.004478 0.000000 0.995522 0.000000 0.097015 0.874627 0.000000 0.028358 0.010448 0.000000 0.000000 0.989552 0.040299 0.001493 0.956716 0.001493 0.029851 0.020896 0.931343 0.017910 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTTGSCCAGGCTGG MEME-3 regular expression -------------------------------------------------------------------------------- TGT[TC][GA][CG]CCAGGCTGG -------------------------------------------------------------------------------- Time 790.85 secs. ******************************************************************************** ******************************************************************************** MOTIF GTAGAGAYRGGGTTT MEME-4 width = 15 sites = 511 llr = 8076 E-value = 2.0e-087 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTAGAGAYRGGGTTT MEME-4 Description -------------------------------------------------------------------------------- Simplified A ::8:a:a:312:::: pos.-specific C :::::::6:::::2: probability G 8:19:a::6989::: matrix T 2a2::::3:::1a8a bits 2.4 * * 2.2 * * * * 1.9 * * * * * 1.7 * * * * * Relative 1.4 ** *** *** Entropy 1.2 ****** * **** (22.8 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GTAGAGACGGGGTTT consensus TA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAGAGAYRGGGTTT MEME-4 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 13.3865 E= 2.0e-087 -241 -632 132 -3 -658 -632 -1564 240 205 -1564 -227 -26 -278 -362 160 -558 234 -532 -332 -426 -234 -473 161 -1564 238 -1564 -532 -358 -558 105 -451 84 89 -532 103 -458 -50 -731 146 -558 -5 -473 135 -458 -226 -573 153 -188 -1564 -1564 -632 241 -658 -48 -1564 204 -1564 -400 -1564 238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAGAGAYRGGGTTT MEME-4 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 511 E= 2.0e-087 0.035225 0.003914 0.776908 0.183953 0.001957 0.003914 0.000000 0.994129 0.778865 0.000000 0.064579 0.156556 0.027397 0.025440 0.943249 0.003914 0.951076 0.007828 0.031311 0.009785 0.037182 0.011742 0.951076 0.000000 0.976517 0.000000 0.007828 0.015656 0.003914 0.645793 0.013699 0.336595 0.348337 0.007828 0.636008 0.007828 0.133072 0.001957 0.861057 0.003914 0.181996 0.011742 0.798434 0.007828 0.039139 0.005871 0.904110 0.050881 0.000000 0.000000 0.003914 0.996086 0.001957 0.223092 0.000000 0.774951 0.000000 0.019569 0.000000 0.980431 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTAGAGAYRGGGTTT MEME-4 regular expression -------------------------------------------------------------------------------- GTAGAGA[CT][GA]GGGT[TC]T -------------------------------------------------------------------------------- Time 1031.85 secs. ******************************************************************************** ******************************************************************************** MOTIF GCCTCRGCCTCCCAA MEME-5 width = 15 sites = 666 llr = 9888 E-value = 1.3e-080 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCTCRGCCTCCCAA MEME-5 Description -------------------------------------------------------------------------------- Simplified A 3::::5:::::::79 pos.-specific C :99:8::aa:aa8:: probability G 7::::4a::::::31 matrix T :1:a21:::a::2:: bits 2.4 * 2.2 * * 1.9 * * 1.7 * ** * Relative 1.4 *** ****** * Entropy 1.2 *** ********* (21.4 bits) 1.0 ***** ********* 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCCTCAGCCTCCCAA consensus A G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTCRGCCTCCCAA MEME-5 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 12.9209 E= 1.3e-080 43 -1602 121 -297 -1602 158 -1602 -154 -696 160 -611 -206 -1602 -370 -1602 238 -497 137 -489 -10 152 -770 29 -127 -464 -453 165 -696 -1602 161 -453 -244 -1602 166 -770 -438 -397 -1602 -1602 240 -597 161 -511 -244 -696 161 -770 -211 -1602 140 -1602 -8 182 -1602 9 -597 222 -411 -153 -1602 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTCRGCCTCCCAA MEME-5 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 666 E= 1.3e-080 0.252252 0.000000 0.723724 0.024024 0.000000 0.935435 0.000000 0.064565 0.001502 0.948949 0.004505 0.045045 0.000000 0.024024 0.000000 0.975976 0.006006 0.807808 0.010511 0.175676 0.539039 0.001502 0.381381 0.078078 0.007508 0.013514 0.977477 0.001502 0.000000 0.951952 0.013514 0.034535 0.000000 0.989489 0.001502 0.009009 0.012012 0.000000 0.000000 0.987988 0.003003 0.953453 0.009009 0.034535 0.001502 0.953453 0.001502 0.043544 0.000000 0.822823 0.000000 0.177177 0.665165 0.000000 0.331832 0.003003 0.873874 0.018018 0.108108 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCTCRGCCTCCCAA MEME-5 regular expression -------------------------------------------------------------------------------- [GA]CCTC[AG]GCCTCCC[AG]A -------------------------------------------------------------------------------- Time 1271.74 secs. ******************************************************************************** ******************************************************************************** MOTIF GCYGGGCRTGGTGGC MEME-6 width = 15 sites = 632 llr = 8434 E-value = 1.2e-062 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCYGGGCRTGGTGGC MEME-6 Description -------------------------------------------------------------------------------- Simplified A :::3:::4:2::::: pos.-specific C :a6:::7:3:::::8 probability G a::79a:6:8a:aa: matrix T ::4:::3:7::a::2 bits 2.4 * 2.2 * 1.9 * 1.7 * Relative 1.4 ** ** **** Entropy 1.2 ** ** ******* (19.3 bits) 1.0 ** **** ******* 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GCCGGGCGTGGTGGC consensus TA TAC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGGGCRTGGTGGC MEME-6 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 12.7594 E= 1.2e-062 -389 -604 164 -389 -1595 162 -604 -231 -289 96 -504 94 75 -662 113 -1595 -208 -1595 159 -357 -214 -1595 162 -1595 -457 122 -530 44 92 -504 96 -280 -343 -16 -1595 191 -20 -530 141 -1595 -243 -482 161 -1595 -1595 -762 -504 240 -243 -1595 162 -589 -372 -662 164 -389 -1595 138 -762 -1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGGGCRTGGTGGC MEME-6 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 632 E= 1.2e-062 0.012658 0.004747 0.969937 0.012658 0.000000 0.957278 0.004747 0.037975 0.025316 0.606013 0.009494 0.359177 0.314873 0.003165 0.681962 0.000000 0.044304 0.000000 0.939873 0.015823 0.042722 0.000000 0.957278 0.000000 0.007911 0.729430 0.007911 0.254747 0.354430 0.009494 0.609177 0.026899 0.017405 0.278481 0.000000 0.704114 0.162975 0.007911 0.829114 0.000000 0.034810 0.011076 0.954114 0.000000 0.000000 0.001582 0.009494 0.988924 0.034810 0.000000 0.962025 0.003165 0.014241 0.003165 0.969937 0.012658 0.000000 0.811709 0.001582 0.186709 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCYGGGCRTGGTGGC MEME-6 regular expression -------------------------------------------------------------------------------- GC[CT][GA]GG[CT][GA][TC]GGTGGC -------------------------------------------------------------------------------- Time 1508.66 secs. ******************************************************************************** ******************************************************************************** MOTIF AACTCCTGRSCTCAR MEME-7 width = 15 sites = 404 llr = 6247 E-value = 1.6e-047 ******************************************************************************** -------------------------------------------------------------------------------- Motif AACTCCTGRSCTCAR MEME-7 Description -------------------------------------------------------------------------------- Simplified A 97:::::16::::96 pos.-specific C :2a:a91::68:a:: probability G 1::::::943:::13 matrix T :1:a:19:::2a::1 bits 2.4 2.2 * * * 1.9 * * * * * 1.7 * ** * * * Relative 1.4 * ****** *** Entropy 1.2 * ******* *** (22.3 bits) 1.0 ********* **** 0.7 ********* ***** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AACTCCTGACCTCAA consensus GG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTCCTGRSCTCAR MEME-7 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 13.4986 E= 1.6e-047 233 -1530 -252 -1530 195 -91 -328 -129 -1530 168 -1530 -1530 -1530 -298 -1530 235 -1530 165 -381 -1530 -466 159 -1530 -185 -466 -198 -1530 228 -185 -1530 159 -466 166 -1530 38 -1530 -254 103 9 -1530 -1530 139 -466 -14 -1530 -398 -1530 238 -1530 164 -1530 -266 226 -1530 -166 -1530 160 -498 0 -79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTCCTGRSCTCAR MEME-7 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 404 E= 1.6e-047 0.945545 0.000000 0.054455 0.000000 0.725248 0.165842 0.032178 0.076733 0.000000 1.000000 0.000000 0.000000 0.000000 0.039604 0.000000 0.960396 0.000000 0.977723 0.022277 0.000000 0.007426 0.940594 0.000000 0.051980 0.007426 0.079208 0.000000 0.913366 0.051980 0.000000 0.940594 0.007426 0.594059 0.000000 0.405941 0.000000 0.032178 0.636139 0.331683 0.000000 0.000000 0.816832 0.012376 0.170792 0.000000 0.019802 0.000000 0.980198 0.000000 0.970297 0.000000 0.029703 0.900990 0.000000 0.099010 0.000000 0.569307 0.009901 0.311881 0.108911 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AACTCCTGRSCTCAR MEME-7 regular expression -------------------------------------------------------------------------------- AACTCCTG[AG][CG]CTCA[AG] -------------------------------------------------------------------------------- Time 1745.85 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTYRGCTCACTGCA MEME-8 width = 15 sites = 231 llr = 3970 E-value = 3.6e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTYRGCTCACTGCA MEME-8 Description -------------------------------------------------------------------------------- Simplified A ::2:3::::a::::a pos.-specific C :a:6::a:a:9::9: probability G ::::7a::::::a:: matrix T a:84:::a:::9::: bits 2.4 * * 2.2 * * * * 1.9 * * * * * 1.7 * * * * * * Relative 1.4 *** ***** ** * Entropy 1.2 *** ********** (24.8 bits) 1.0 *************** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TCTCGGCTCACTGCA consensus ATA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTYRGCTCACTGCA MEME-8 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 14.3494 E= 3.6e-018 -1450 -300 -1450 236 -344 165 -1450 -1450 12 -517 -1450 207 -1450 98 -1450 104 83 -1450 109 -1450 -263 -1450 164 -1450 -1450 165 -417 -1450 -1450 -1450 -1450 241 -1450 162 -1450 -212 236 -317 -1450 -1450 -1450 158 -385 -212 -312 -271 -1450 231 -227 -1450 162 -1450 -212 155 -1450 -212 241 -1450 -1450 -1450 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTYRGCTCACTGCA MEME-8 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 231 E= 3.6e-018 0.000000 0.038961 0.000000 0.961039 0.017316 0.982684 0.000000 0.000000 0.203463 0.008658 0.000000 0.787879 0.000000 0.614719 0.000000 0.385281 0.333333 0.000000 0.666667 0.000000 0.030303 0.000000 0.969697 0.000000 0.000000 0.982684 0.017316 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.956710 0.000000 0.043290 0.965368 0.034632 0.000000 0.000000 0.000000 0.935065 0.021645 0.043290 0.021645 0.047619 0.000000 0.930736 0.038961 0.000000 0.961039 0.000000 0.043290 0.913420 0.000000 0.043290 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTYRGCTCACTGCA MEME-8 regular expression -------------------------------------------------------------------------------- TC[TA][CT][GA]GCTCACTGCA -------------------------------------------------------------------------------- Time 1980.75 secs. ******************************************************************************** ******************************************************************************** MOTIF GGCGGSGGCGGSGGC MEME-9 width = 15 sites = 868 llr = 8819 E-value = 7.3e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-9 Description -------------------------------------------------------------------------------- Simplified A 1:11::1:1:1:::: pos.-specific C 1:7216::8217::8 probability G 89:7949a:783991 matrix T ::11::::1:::::: bits 2.4 2.2 1.9 1.7 Relative 1.4 * * * Entropy 1.2 * * ** ** (14.7 bits) 1.0 * * *** * *** 0.7 *** *********** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel GGCGGCGGCGGCGGC consensus G C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-9 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 12.5938 E= 7.3e-018 -130 -127 135 -1641 -226 -462 160 -1641 -69 124 -1641 -36 -126 -92 115 -159 -1641 -159 152 -1641 -1641 96 34 -1641 -189 -399 157 -1641 -1641 -438 162 -283 -157 137 -491 -66 -389 -45 124 -318 -137 -235 142 -259 -535 109 9 -1641 -1641 -291 156 -222 -1641 -276 159 -403 -1641 141 -122 -239 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-9 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 868 E= 7.3e-018 0.076037 0.129032 0.794931 0.000000 0.039171 0.012673 0.948157 0.000000 0.116359 0.737327 0.000000 0.146313 0.078341 0.164747 0.694700 0.062212 0.000000 0.103687 0.896313 0.000000 0.000000 0.605991 0.394009 0.000000 0.050691 0.019585 0.929724 0.000000 0.000000 0.014977 0.958525 0.026498 0.063364 0.807604 0.010369 0.118664 0.012673 0.229263 0.737327 0.020737 0.072581 0.061060 0.835253 0.031106 0.004608 0.662442 0.332949 0.000000 0.000000 0.041475 0.918203 0.040323 0.000000 0.046083 0.942396 0.011521 0.000000 0.830645 0.133641 0.035714 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGCGGSGGCGGSGGC MEME-9 regular expression -------------------------------------------------------------------------------- GGCGG[CG]GGC[GC]G[CG]GGC -------------------------------------------------------------------------------- Time 2214.09 secs. ******************************************************************************** ******************************************************************************** MOTIF TCRYGCCACTGCACT MEME-10 width = 15 sites = 220 llr = 3459 E-value = 1.1e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCRYGCCACTGCACT MEME-10 Description -------------------------------------------------------------------------------- Simplified A ::3:3::a::::a:: pos.-specific C :7:5:aa:9::9:a: probability G :16:7:::::9:::: matrix T a3:4::::1a:1::a bits 2.4 * * 2.2 * * * * * 1.9 * * * * * 1.7 * * * * * Relative 1.4 * *** ****** Entropy 1.2 * ********** (22.7 bits) 1.0 * *********** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TCGCGCCACTGCACT consensus TATA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRYGCCACTGCACT MEME-10 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1231606 bayes= 14.4042 E= 1.1e-011 -437 -1443 -1443 240 -1443 110 -264 59 76 -278 103 -1443 -337 71 -352 125 51 -1443 123 -1443 -1443 162 -1443 -220 -1443 165 -1443 -337 240 -1443 -510 -1443 -1443 147 -1443 -46 -437 -329 -1443 235 -205 -1443 160 -437 -1443 159 -1443 -167 235 -1443 -329 -378 -378 162 -1443 -278 -378 -310 -1443 234 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRYGCCACTGCACT MEME-10 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 220 E= 1.1e-011 0.009091 0.000000 0.000000 0.990909 0.000000 0.668182 0.050000 0.281818 0.318182 0.045455 0.636364 0.000000 0.018182 0.509091 0.027273 0.445455 0.268182 0.000000 0.731818 0.000000 0.000000 0.959091 0.000000 0.040909 0.000000 0.981818 0.000000 0.018182 0.990909 0.000000 0.009091 0.000000 0.000000 0.863636 0.000000 0.136364 0.009091 0.031818 0.000000 0.959091 0.045455 0.000000 0.945455 0.009091 0.000000 0.940909 0.000000 0.059091 0.954545 0.000000 0.031818 0.013636 0.013636 0.959091 0.000000 0.027273 0.013636 0.036364 0.000000 0.950000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCRYGCCACTGCACT MEME-10 regular expression -------------------------------------------------------------------------------- T[CT][GA][CT][GA]CCACTGCACT -------------------------------------------------------------------------------- Time 2441.97 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (10) found. ******************************************************************************** CPU: cn45 ********************************************************************************