******************************************************************************** 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= seqs/AT2G24430_peak_sequences.fasta 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 seqs/AT2G24430_peak_sequences.fasta -dna -oc out/AT2G24430 -nostatus -time 300 -mod zoops -nmotifs 2 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 -mpi model: mod= zoops nmotifs= 2 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= 50 nsites: minsites= 2 maxsites= 2495 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= 647935 N= 2495 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.353 C 0.147 G 0.147 T 0.353 Background letter frequencies (from file dataset with add-one prior applied): A 0.354 C 0.146 G 0.146 T 0.354 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GDTWDCKTGTDDWWBAAGWHA MEME-1 width = 21 sites = 2378 llr = 19728 E-value = 6.8e-280 ******************************************************************************** -------------------------------------------------------------------------------- Motif GDTWDCKTGTDDWWBAAGWHA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 23135:::2244451652347 pos.-specific C 11:::a:::111113:2:22: probability G 53:12:5:81232221261:: matrix T 23963:5a:622334311443 bits 2.8 * 2.5 * 2.2 * 1.9 * Relative 1.7 * * Entropy 1.4 * ** (12.0 bits) 1.1 * **** 0.8 * **** * 0.6 * * **** * * 0.3 ********** **** * 0.0 --------------------- Multilevel GATTACGTGTAAAATAAGTTA consensus G AT T TGTTCT AAAT sequence T G GT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDTWDCKTGTDDWWBAAGWHA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 598035 bayes= 9.77799 E= 6.8e-280 -89 -11 173 -90 -13 -96 114 -34 -157 -1786 -1786 132 -24 -1786 -3 66 36 -202 65 -34 -739 277 -1786 -1786 -1786 -1786 184 43 -1786 -1786 -1786 150 -100 -263 245 -1786 -108 1 -112 81 8 -16 76 -51 13 1 82 -77 13 -2 34 -32 38 -96 11 -20 -130 108 42 -1 82 -263 -128 -28 62 43 23 -202 -82 -323 213 -129 -5 15 -11 3 11 45 -214 12 96 -221 -277 -46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDTWDCKTGTDDWWBAAGWHA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2378 E= 6.8e-280 0.190917 0.135408 0.484441 0.189235 0.322960 0.075273 0.322960 0.278806 0.119428 0.000000 0.000000 0.880572 0.298991 0.000000 0.143398 0.557611 0.454163 0.036165 0.230025 0.279647 0.002103 0.997897 0.000000 0.000000 0.000000 0.000000 0.523129 0.476871 0.000000 0.000000 0.000000 1.000000 0.176619 0.023549 0.799832 0.000000 0.167368 0.147183 0.067283 0.618167 0.373423 0.130782 0.247267 0.248528 0.388141 0.146762 0.258200 0.206897 0.386880 0.144239 0.185029 0.283852 0.459630 0.075273 0.157275 0.307822 0.143818 0.309083 0.195122 0.351976 0.625736 0.023549 0.060135 0.290580 0.543314 0.197645 0.171993 0.087048 0.201009 0.015559 0.639193 0.144239 0.341884 0.161901 0.135828 0.360387 0.382675 0.199748 0.033221 0.384357 0.689235 0.031539 0.021447 0.257780 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GDTWDCKTGTDDWWBAAGWHA MEME-1 regular expression -------------------------------------------------------------------------------- G[AGT]T[TA][ATG]C[GT]TGT[ATG][AGT][AT][AT][TC][AT]A[GA][TA][TA][AT] -------------------------------------------------------------------------------- Time 118.32 secs. ******************************************************************************** ******************************************************************************** MOTIF BTTTTTTTTTYTTYTTTTTBW MEME-2 width = 21 sites = 578 llr = 5833 E-value = 1.9e-006 ******************************************************************************** -------------------------------------------------------------------------------- Motif BTTTTTTTTTYTTYTTTTTBW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 11:::1::::::::::::112 pos.-specific C 3:313131213:231131232 probability G 2:1:1:111:1:111:12132 matrix T 39697868695a868967644 bits 2.8 2.5 2.2 1.9 Relative 1.7 Entropy 1.4 * (14.6 bits) 1.1 * * * 0.8 **** ** * ** ** * 0.6 ***************** * 0.3 ******************** 0.0 --------------------- Multilevel TTTTTTTTTTTTTTTTTTTTT consensus C C C C C C C CG CA sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTTTTTTTTTYTTYTTTTTBW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 598035 bayes= 12.2588 E= 1.9e-006 -165 117 64 -10 -182 -170 -1582 127 -1582 93 -97 87 -1582 -73 -159 129 -1582 81 -88 91 -222 -36 -270 115 -1582 96 -38 77 -1582 -21 -38 111 -1582 71 -29 86 -387 -88 -1582 134 -287 122 -6 41 -377 -1582 -1582 146 -1582 18 -119 112 -535 112 -29 65 -435 -131 -70 124 -1582 -38 -1582 133 -468 84 -1 71 -1582 -45 64 91 -127 7 -12 67 -263 116 79 4 -52 23 12 25 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTTTTTTTTTYTTYTTTTTBW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 578 E= 1.9e-006 0.112457 0.328720 0.228374 0.330450 0.100346 0.044983 0.000000 0.854671 0.000000 0.278547 0.074394 0.647059 0.000000 0.088235 0.048443 0.863322 0.000000 0.256055 0.079585 0.664360 0.076125 0.114187 0.022491 0.787197 0.000000 0.283737 0.112457 0.603806 0.000000 0.126298 0.112457 0.761246 0.000000 0.238754 0.119377 0.641869 0.024221 0.079585 0.000000 0.896194 0.048443 0.340830 0.140138 0.470588 0.025952 0.000000 0.000000 0.974048 0.000000 0.166090 0.064014 0.769896 0.008651 0.318339 0.119377 0.553633 0.017301 0.058824 0.089965 0.833910 0.000000 0.112457 0.000000 0.887543 0.013841 0.261246 0.145329 0.579585 0.000000 0.107266 0.228374 0.664360 0.147059 0.153979 0.134948 0.564014 0.057093 0.326990 0.252595 0.363322 0.247405 0.171280 0.159170 0.422145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BTTTTTTTTTYTTYTTTTTBW MEME-2 regular expression -------------------------------------------------------------------------------- [TCG]T[TC]T[TC]T[TC]T[TC]T[TC]TT[TC]TT[TC][TG]T[TCG][TA] -------------------------------------------------------------------------------- Time 221.38 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************