******************************************************************************** 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/AT2G03500_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/AT2G03500_peak_sequences.fasta -dna -oc out/AT2G03500 -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= 3317 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= 555938 N= 3317 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.329 C 0.171 G 0.171 T 0.329 Background letter frequencies (from file dataset with add-one prior applied): A 0.331 C 0.169 G 0.169 T 0.331 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WNRGAATMTTCNWW MEME-1 width = 14 sites = 3236 llr = 24860 E-value = 4.6e-466 ******************************************************************************** -------------------------------------------------------------------------------- Motif WNRGAATMTTCNWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 434:9a:6:21243 pos.-specific C 221::::4:27212 probability G 123a:::::1:321 matrix T 332:::a:a61334 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.5 * ** * Entropy 1.3 **** * (11.1 bits) 1.0 ****** * 0.8 ****** * 0.5 ****** * 0.3 ********* 0.0 -------------- Multilevel AAAGAATATTCTAT consensus TTG C A GTA sequence G A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WNRGAATMTTCNWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 512817 bayes= 8.91962 E= 4.6e-466 29 -5 -35 -15 -6 2 45 -25 42 -102 91 -109 -1830 -1830 256 -1830 152 -1830 -334 -326 157 -1830 -1830 -428 -1830 -1830 -1830 160 88 120 -1830 -1830 -467 -1830 -1830 158 -57 -16 -136 76 -203 210 -187 -118 -47 21 63 -12 32 -63 16 -19 -13 11 -62 29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WNRGAATMTTCNWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 3236 E= 4.6e-466 0.403894 0.163782 0.133189 0.299135 0.318294 0.171817 0.231150 0.278739 0.442522 0.083436 0.318294 0.155748 0.000000 0.000000 1.000000 0.000000 0.948702 0.000000 0.016687 0.034611 0.983004 0.000000 0.000000 0.016996 0.000000 0.000000 0.000000 1.000000 0.610012 0.389988 0.000000 0.000000 0.012979 0.000000 0.000000 0.987021 0.222188 0.151112 0.066131 0.560569 0.081273 0.726514 0.046354 0.145859 0.238875 0.195612 0.261743 0.303770 0.412237 0.109085 0.189122 0.289555 0.301298 0.182942 0.110321 0.405439 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WNRGAATMTTCNWW MEME-1 regular expression -------------------------------------------------------------------------------- [AT][ATG][AG]GAAT[AC]T[TA]C[TGA][AT][TA] -------------------------------------------------------------------------------- Time 123.75 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTAGATCCAATAAG MEME-2 width = 50 sites = 20 llr = 1228 E-value = 2.0e-053 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTAGATCCAATAAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::11:::a:1::a12aaa:::::1a::a:::1:::::a2a:::aa:aa: pos.-specific C ::::9::9::::::::::::a::::::::999::9:::::::9a::1::: probability G :::a1::::a::::99::::::::a::a::::a::::::8:::::::::a matrix T aaa:1aa1::aaa::::::a:aaa::a::111:a1aaa:::a21::a::: bits 2.6 * * * * 2.3 * * * * * * * * 2.1 * * * * * * * **** * * * 1.8 * * * ** * * * **** * ** * Relative 1.5 ********** *********************************** *** Entropy 1.3 ************************************************** (88.6 bits) 1.0 ************************************************** 0.8 ************************************************** 0.5 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTAGATCCAATAAG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTAGATCCAATAAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 393405 bayes= 14.5152 E= 2.0e-053 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -272 -1097 249 -1097 -272 233 -176 -272 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -1097 241 -1097 -172 160 -1097 -1097 -1097 -1097 -1097 256 -1097 -272 -1097 -1097 152 -1097 -1097 -1097 160 -1097 -1097 -1097 160 160 -1097 -1097 -1097 -172 -1097 241 -1097 -114 -1097 233 -1097 160 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -1097 -1097 -1097 -1097 -1097 -1097 160 -1097 256 -1097 -1097 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -272 -1097 249 -1097 160 -1097 -1097 -1097 -1097 -1097 -1097 160 -1097 -1097 256 -1097 160 -1097 -1097 -1097 -1097 241 -1097 -172 -1097 241 -1097 -172 -1097 241 -1097 -172 -272 -1097 249 -1097 -1097 -1097 -1097 160 -1097 241 -1097 -172 -1097 -1097 -1097 160 -1097 -1097 -1097 160 -1097 -1097 -1097 160 160 -1097 -1097 -1097 -73 -1097 224 -1097 160 -1097 -1097 -1097 -1097 -1097 -1097 160 -1097 233 -1097 -114 -1097 249 -1097 -272 160 -1097 -1097 -1097 160 -1097 -1097 -1097 -1097 -176 -1097 152 160 -1097 -1097 -1097 160 -1097 -1097 -1097 -1097 -1097 256 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTAGATCCAATAAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 20 E= 2.0e-053 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.050000 0.000000 0.950000 0.000000 0.050000 0.850000 0.050000 0.050000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.900000 0.000000 0.100000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.050000 0.000000 0.000000 0.950000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.150000 0.000000 0.850000 0.000000 1.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 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 0.050000 0.000000 0.950000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.050000 0.000000 0.950000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.850000 0.000000 0.150000 0.000000 0.950000 0.000000 0.050000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.050000 0.000000 0.950000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTAGATCCAATAAG MEME-2 regular expression -------------------------------------------------------------------------------- TTTGCTTCAGTTTAGGAAATCTTTGATGACCCGTCTTTA[GA]ATCCAATAAG -------------------------------------------------------------------------------- Time 227.82 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************