******************************************************************************** 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/AT5G47230_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/AT5G47230_peak_sequences.fasta -dna -oc out/AT5G47230 -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= 1070 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= 187770 N= 1070 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.239 C 0.261 G 0.261 T 0.239 Background letter frequencies (from file dataset with add-one prior applied): A 0.239 C 0.261 G 0.261 T 0.239 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HDRYGGCGGCGGHGR MEME-1 width = 15 sites = 1024 llr = 10038 E-value = 6.4e-875 ******************************************************************************** -------------------------------------------------------------------------------- Motif HDRYGGCGGCGGHGR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3331:1:::1:2423 pos.-specific C 3116::a::9:2311 probability G 145:a9:aa:96155 matrix T 3313::::::1:221 bits 2.1 1.9 * *** 1.7 * *** 1.4 * **** Relative 1.2 ******* Entropy 1.0 ******* (14.1 bits) 0.8 ******** 0.6 ******** 0.4 ********** * 0.2 *************** 0.0 --------------- Multilevel TGGCGGCGGCGGAGG consensus CTAT CAA sequence AA T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDRYGGCGGCGGHGR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 172790 bayes= 8.13049 E= 6.4e-875 16 28 -193 54 14 -164 57 15 28 -145 98 -125 -161 118 -1664 47 -1664 -1664 193 -593 -96 -525 173 -593 -1664 190 -1664 -313 -793 -1664 192 -447 -635 -1664 193 -1664 -210 183 -1664 -385 -693 -460 171 -85 -31 -64 120 -265 59 37 -143 -21 -6 -223 106 -48 12 -140 93 -71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDRYGGCGGCGGHGR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1024 E= 6.4e-875 0.267578 0.317383 0.068359 0.346680 0.263672 0.083984 0.386719 0.265625 0.290039 0.095703 0.513672 0.100586 0.078125 0.591797 0.000000 0.330078 0.000000 0.000000 0.996094 0.003906 0.123047 0.006836 0.866211 0.003906 0.000000 0.972656 0.000000 0.027344 0.000977 0.000000 0.988281 0.010742 0.002930 0.000000 0.997070 0.000000 0.055664 0.927734 0.000000 0.016602 0.001953 0.010742 0.854492 0.132812 0.193359 0.166992 0.601562 0.038086 0.359375 0.337891 0.096680 0.206055 0.229492 0.055664 0.543945 0.170898 0.258789 0.098633 0.496094 0.146484 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDRYGGCGGCGGHGR MEME-1 regular expression -------------------------------------------------------------------------------- [TCA][GTA][GA][CT]GGCGGCGG[ACT][GA][GA] -------------------------------------------------------------------------------- Time 77.55 secs. ******************************************************************************** ******************************************************************************** MOTIF GHGGHGGAGRMGGAGRARGAG MEME-2 width = 21 sites = 498 llr = 4813 E-value = 3.1e-182 ******************************************************************************** -------------------------------------------------------------------------------- Motif GHGGHGGAGRMGGAGRARGAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 241342352352361353362 pos.-specific C :3::3::2:13::21:2::21 probability G 6:87176:76:77:86167:6 matrix T 131:21121:21:2::21:22 bits 2.1 1.9 1.7 1.4 Relative 1.2 Entropy 1.0 ** * * (13.9 bits) 0.8 ** * ** ** ** 0.6 * ** ** ** ** ** *** 0.4 **** *********** **** 0.2 ********************* 0.0 --------------------- Multilevel GAGGAGGAGGAGGAGGAGGAG consensus AT AC ACAACAAC A AATT sequence C T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHGGHGGAGRMGGAGRARGAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 166370 bayes= 10.5306 E= 3.1e-182 -6 -1560 126 -72 75 4 -1560 46 -83 -1560 156 -134 37 -502 136 -431 78 14 -181 -6 -40 -332 142 -134 20 -256 124 -194 116 -7 -356 -28 5 -1560 139 -181 42 -160 117 -531 102 1 -244 -22 2 -1560 142 -204 41 -1560 139 -1560 128 -35 -263 -47 -83 -207 162 -1560 55 -402 121 -299 101 -50 -91 -29 47 -702 123 -219 23 -244 134 -489 128 -50 -1560 -1 -55 -222 114 -22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHGGHGGAGRMGGAGRARGAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 498 E= 3.1e-182 0.228916 0.000000 0.626506 0.144578 0.401606 0.269076 0.000000 0.329317 0.134538 0.000000 0.771084 0.094378 0.309237 0.008032 0.670683 0.012048 0.409639 0.287149 0.074297 0.228916 0.180723 0.026104 0.698795 0.094378 0.275100 0.044177 0.618474 0.062249 0.532129 0.248996 0.022088 0.196787 0.246988 0.000000 0.684739 0.068273 0.319277 0.086345 0.588353 0.006024 0.483936 0.263052 0.048193 0.204819 0.242972 0.000000 0.698795 0.058233 0.317269 0.000000 0.682731 0.000000 0.580321 0.204819 0.042169 0.172691 0.134538 0.062249 0.803213 0.000000 0.349398 0.016064 0.604418 0.030120 0.481928 0.184739 0.138554 0.194779 0.331325 0.002008 0.614458 0.052209 0.281124 0.048193 0.662651 0.008032 0.578313 0.184739 0.000000 0.236948 0.162651 0.056225 0.576305 0.204819 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHGGHGGAGRMGGAGRARGAG MEME-2 regular expression -------------------------------------------------------------------------------- [GA][ATC]G[GA][ACT]G[GA][AC][GA][GA][ACT][GA][GA][AC]G[GA]A[GA][GA][AT][GT] -------------------------------------------------------------------------------- Time 144.89 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************