******************************************************************************** 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/AT1G01060_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/AT1G01060_peak_sequences.fasta -dna -oc out/AT1G01060 -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= 5492 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= 1389174 N= 5492 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.375 C 0.125 G 0.125 T 0.375 Background letter frequencies (from file dataset with add-one prior applied): A 0.376 C 0.124 G 0.124 T 0.376 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGATATTTTT MEME-1 width = 10 sites = 5484 llr = 40013 E-value = 1.1e-172 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGATATTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7:a:8::122 pos.-specific C ::::::::11 probability G 1a::::::12 matrix T 2::a2aa965 bits 3.0 2.7 * 2.4 * 2.1 * Relative 1.8 * Entropy 1.5 ** (10.5 bits) 1.2 *** ** 0.9 *** *** 0.6 ******** 0.3 ********* 0.0 ---------- Multilevel AGATATTTTT consensus AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATATTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1339744 bayes= 9.87788 E= 1.1e-172 98 -533 -37 -124 -445 -1906 296 -492 141 -1906 -1906 -1100 -1001 -1906 -294 139 111 -841 -1906 -100 -1906 -661 -358 140 -469 -783 -625 139 -220 -1906 -1906 129 -87 -61 -17 68 -81 22 33 37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATATTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5484 E= 1.1e-172 0.741247 0.003100 0.096280 0.159373 0.017141 0.000000 0.970460 0.012400 0.999818 0.000000 0.000000 0.000182 0.000365 0.000000 0.016229 0.983406 0.812363 0.000365 0.000000 0.187272 0.000000 0.001276 0.010394 0.988330 0.014588 0.000547 0.001641 0.983224 0.081875 0.000000 0.000000 0.918125 0.205872 0.081327 0.110321 0.602480 0.214260 0.144785 0.156455 0.484500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATATTTTT MEME-1 regular expression -------------------------------------------------------------------------------- AGATATTT[TA][TA] -------------------------------------------------------------------------------- Time 119.99 secs. ******************************************************************************** ******************************************************************************** MOTIF TAAATATTTTGGAAGTTTTATTTTAGTAACTAATCGTGTAGTTAATGTRG MEME-2 width = 50 sites = 40 llr = 2173 E-value = 8.3e-080 ******************************************************************************** -------------------------------------------------------------------------------- Motif TAAATATTTTGGAAGTTTTATTTTAGTAACTAATCGTGTAGTTAATGTRG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :aaa:a::::22aa::21:a::::a1:aa2:aa::::::a:::aa:::41 pos.-specific C :::::::::1:::::::::::::::::::61:::9::::::::::::::: probability G ::::::::::88::a::::::::::9:::::::::a:a::a::::2a:69 matrix T a:::a:aaa9:::::a9aa:aaaa::a::29::a1:a:a::aa::9:a:: bits 3.0 * * * 2.7 * * * * * 2.4 * * ** * * * * 2.1 * * ** * * * * Relative 1.8 ** * * ** * * * * Entropy 1.5 * **** * ***** * *** ** ** ********** ** ** * (78.4 bits) 1.2 **************** ************ *************** **** 0.9 ************************************************** 0.6 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel TAAATATTTTGGAAGTTTTATTTTAGTAACTAATCGTGTAGTTAATGTGG consensus AA A A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAAATATTTTGGAAGTTTTATTTTAGTAACTAATCGTGTAGTTAATGTRG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 1120064 bayes= 16.2471 E= 8.3e-080 -1197 -1197 -1197 141 138 -1197 -1197 -390 141 -1197 -1197 -1197 141 -1197 -1197 -1197 -1197 -1197 -1197 141 141 -1197 -1197 -1197 -390 -1197 -1197 138 -1197 -1197 -231 138 -1197 -1197 -1197 141 -1197 -32 -1197 126 -91 -1197 264 -390 -74 -1197 264 -1197 141 -1197 -1197 -1197 141 -1197 -1197 -1197 -390 -1197 297 -1197 -1197 -1197 -231 138 -132 -1197 -1197 118 -291 -1197 -1197 134 -1197 -1197 -1197 141 138 -1197 -231 -1197 -1197 -1197 -1197 141 -1197 -1197 -1197 141 -1197 -1197 -1197 141 -1197 -231 -1197 138 141 -1197 -1197 -1197 -291 -1197 289 -390 -1197 -1197 -231 138 141 -1197 -1197 -1197 141 -1197 -1197 -1197 -91 227 -1197 -91 -1197 1 -1197 122 141 -1197 -1197 -1197 141 -1197 -1197 -1197 -1197 -1197 -1197 141 -1197 285 -1197 -191 -1197 -1197 301 -1197 -1197 -1197 -1197 141 -1197 -1197 301 -1197 -1197 -1197 -1197 141 141 -1197 -1197 -1197 -1197 -1197 301 -1197 -1197 -1197 -231 138 -1197 -1197 -1197 141 141 -1197 -1197 -1197 138 -1197 -1197 -390 -1197 -1197 27 118 -390 -1197 297 -1197 -1197 -1197 -1197 141 -10 -1197 233 -390 -232 -1197 289 -1197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAAATATTTTGGAAGTTTTATTTTAGTAACTAATCGTGTAGTTAATGTRG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 40 E= 8.3e-080 0.000000 0.000000 0.000000 1.000000 0.975000 0.000000 0.000000 0.025000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.025000 0.000000 0.000000 0.975000 0.000000 0.000000 0.025000 0.975000 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.000000 0.900000 0.200000 0.000000 0.775000 0.025000 0.225000 0.000000 0.775000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.025000 0.000000 0.975000 0.000000 0.000000 0.000000 0.025000 0.975000 0.150000 0.000000 0.000000 0.850000 0.050000 0.000000 0.000000 0.950000 0.000000 0.000000 0.000000 1.000000 0.975000 0.000000 0.025000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.025000 0.000000 0.975000 1.000000 0.000000 0.000000 0.000000 0.050000 0.000000 0.925000 0.025000 0.000000 0.000000 0.025000 0.975000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.125000 0.000000 0.875000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.025000 0.975000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.975000 0.000000 0.000000 0.025000 0.000000 0.000000 0.150000 0.850000 0.025000 0.000000 0.975000 0.000000 0.000000 0.000000 0.000000 1.000000 0.350000 0.000000 0.625000 0.025000 0.075000 0.000000 0.925000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TAAATATTTTGGAAGTTTTATTTTAGTAACTAATCGTGTAGTTAATGTRG MEME-2 regular expression -------------------------------------------------------------------------------- TAAATATTTT[GA][GA]AAGTTTTATTTTAGTAA[CAT]TAATCGTGTAGTTAATGT[GA]G -------------------------------------------------------------------------------- Time 231.40 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************