******************************************************************************** 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/AT1G08320_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/AT1G08320_peak_sequences.fasta -dna -oc out/AT1G08320 -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= 1331 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= 223523 N= 1331 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.305 C 0.195 G 0.195 T 0.305 Background letter frequencies (from file dataset with add-one prior applied): A 0.307 C 0.193 G 0.193 T 0.307 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DWTGATGACGTCAYH MEME-1 width = 15 sites = 1265 llr = 12478 E-value = 1.6e-895 ******************************************************************************** -------------------------------------------------------------------------------- Motif DWTGATGACGTCAYH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 44216::a:1:2713 pos.-specific C 11113:::9::6:43 probability G 32171:9::9:2221 matrix T 235::a1:1:a:133 bits 2.4 2.1 1.9 * ** 1.7 ****** Relative 1.4 ****** Entropy 1.2 ****** (14.2 bits) 0.9 * ****** 0.7 * ******** 0.5 ********** 0.2 ************ 0.0 --------------- Multilevel AATGATGACGTCACA consensus GTA C G TC sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWTGATGACGTCAYH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 204889 bayes= 9.39346 E= 1.6e-895 21 -85 61 -34 42 -72 -18 -3 -37 -55 -85 77 -124 -121 194 -277 95 51 -65 -514 -1695 -1695 -1695 171 -1695 -1695 226 -208 170 -1695 -1695 -560 -1695 222 -793 -162 -243 -693 228 -1695 -560 -476 -635 168 -65 161 5 -428 118 -461 -10 -142 -136 94 -10 11 10 52 -47 -27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWTGATGACGTCAYH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1265 E= 1.6e-895 0.354941 0.107510 0.295652 0.241897 0.411067 0.116996 0.170751 0.301186 0.237154 0.132016 0.107510 0.523320 0.129644 0.083794 0.741502 0.045059 0.592095 0.275889 0.123320 0.008696 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.927273 0.072727 0.993676 0.000000 0.000000 0.006324 0.000000 0.899605 0.000791 0.099605 0.056917 0.001581 0.941502 0.000000 0.006324 0.007115 0.002372 0.984190 0.195257 0.588933 0.200000 0.015810 0.697233 0.007905 0.180237 0.114625 0.119368 0.369960 0.180237 0.330435 0.328063 0.277470 0.139921 0.254545 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWTGATGACGTCAYH MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][AT][TA]G[AC]TGACGT[CG]A[CT][ACT] -------------------------------------------------------------------------------- Time 125.18 secs. ******************************************************************************** ******************************************************************************** MOTIF GARRAAGARRRARAARRARAR MEME-2 width = 21 sites = 280 llr = 3030 E-value = 9.2e-072 ******************************************************************************** -------------------------------------------------------------------------------- Motif GARRAAGARRRARAARRARAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 276479395467486557485 pos.-specific C :11:11::1::1:::112::1 probability G 71363171353261343:624 matrix T 11::::::1:1:::1::1:11 bits 2.4 2.1 1.9 1.7 Relative 1.4 Entropy 1.2 * * (15.6 bits) 0.9 * * *** * ** * 0.7 * ***** * **** ** 0.5 ******** ************ 0.2 ********************* 0.0 --------------------- Multilevel GAAGAAGAAGAAGAAAAAGAA consensus GAG A GAGGA GGG A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARRAAGARRRARAARRARAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 196903 bayes= 11.6232 E= 9.2e-072 -75 -230 181 -162 108 -106 -51 -134 85 -59 60 -362 46 -344 154 -1477 115 -151 37 -1477 148 -151 -130 -1477 -27 -295 182 -296 151 -259 -106 -1477 74 -167 55 -107 43 -217 149 -1477 98 -376 67 -203 121 -137 15 -1477 37 -1477 164 -1477 143 -244 -47 -1477 105 -476 55 -203 60 -137 116 -342 79 -90 77 -310 115 -37 -259 -114 32 -276 156 -410 132 -1477 -27 -210 68 -176 90 -178 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARRAAGARRRARAARRARAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 280 E= 9.2e-072 0.182143 0.039286 0.678571 0.100000 0.650000 0.092857 0.135714 0.121429 0.553571 0.128571 0.292857 0.025000 0.421429 0.017857 0.560714 0.000000 0.682143 0.067857 0.250000 0.000000 0.853571 0.067857 0.078571 0.000000 0.253571 0.025000 0.682143 0.039286 0.875000 0.032143 0.092857 0.000000 0.510714 0.060714 0.282143 0.146429 0.414286 0.042857 0.542857 0.000000 0.603571 0.014286 0.307143 0.075000 0.710714 0.075000 0.214286 0.000000 0.396429 0.000000 0.603571 0.000000 0.825000 0.035714 0.139286 0.000000 0.635714 0.007143 0.282143 0.075000 0.464286 0.075000 0.432143 0.028571 0.532143 0.103571 0.328571 0.035714 0.678571 0.150000 0.032143 0.139286 0.382143 0.028571 0.571429 0.017857 0.767857 0.000000 0.160714 0.071429 0.492857 0.057143 0.360714 0.089286 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARRAAGARRRARAARRARAR MEME-2 regular expression -------------------------------------------------------------------------------- GA[AG][GA][AG]A[GA]A[AG][GA][AG][AG][GA]A[AG][AG][AG]A[GA]A[AG] -------------------------------------------------------------------------------- Time 231.05 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************