******************************************************************************** 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/AT1G75240_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/AT1G75240_peak_sequences.fasta -dna -oc out/AT1G75240 -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= 4785 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= 1314920 N= 4785 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.383 C 0.117 G 0.117 T 0.383 Background letter frequencies (from file dataset with add-one prior applied): A 0.383 C 0.117 G 0.117 T 0.383 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTAACAATCTTCCCWAAATCTCTCCACATTAACTACACGA MEME-1 width = 41 sites = 32 llr = 1608 E-value = 8.2e-045 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTAACAATCTTCCCWAAATCTCTCCACATTAACTACACGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::8a:9a:::::::5aaa:::::::a:8::aa::a:a:2a pos.-specific C :::::9::1a::99a:::::a:9:a8:92::::a::a:a:: probability G :::2:::::::::::1:::::::::::::::::::::::8: matrix T aaa::11:9:aa:1:4:::a:a1a:2:1:aa:::a:::::: bits 3.1 * * * * 2.8 * * *** * * * * * 2.5 * * *** * * * * * * * 2.2 * * *** * * * * * * ** Relative 1.9 * * *** * * ** * * * ** Entropy 1.5 * * *** * * ** * * * ** (72.5 bits) 1.2 *** ** ******** ************ ************ 0.9 *************** ************************* 0.6 *************** ************************* 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel TTTAACAATCTTCCCAAAATCTCTCCACATTAACTACACGA consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTAACAATCTTCCCWAAATCTCTCCACATTAACTACACGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 1123519 bayes= 15.8365 E= 8.2e-045 -1164 -1164 -1164 139 -1164 -1164 -1164 139 -1164 -1164 -1164 139 114 -1164 41 -1164 139 -1164 -1164 -1164 -1164 300 -1164 -261 124 -1164 -1164 -203 139 -1164 -1164 -1164 -1164 -91 -1164 129 -1164 305 -1164 -361 -1164 -1164 -1164 139 -1164 -1164 -1164 139 -1164 300 -191 -361 -1164 300 -1164 -261 -1164 309 -1164 -1164 39 -1164 -91 19 139 -1164 -1164 -1164 139 -1164 -1164 -1164 139 -1164 -1164 -1164 -1164 -1164 -1164 139 -1164 309 -1164 -1164 -1164 -1164 -1164 139 -1164 295 -1164 -203 -1164 -1164 -1164 139 -1164 305 -1164 -361 -1164 274 -1164 -81 139 -1164 -1164 -1164 -1164 295 -1164 -203 109 68 -1164 -1164 -1164 -1164 -1164 139 -1164 -1164 -1164 139 139 -1164 -1164 -1164 134 -191 -1164 -1164 -1164 305 -1164 -361 -1164 -1164 -1164 139 139 -1164 -1164 -1164 -1164 309 -1164 -1164 139 -1164 -1164 -1164 -1164 309 -1164 -1164 -129 -1164 285 -1164 134 -1164 -191 -1164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTAACAATCTTCCCWAAATCTCTCCACATTAACTACACGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 32 E= 8.2e-045 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.843750 0.000000 0.156250 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.937500 0.000000 0.062500 0.906250 0.000000 0.000000 0.093750 1.000000 0.000000 0.000000 0.000000 0.000000 0.062500 0.000000 0.937500 0.000000 0.968750 0.000000 0.031250 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.937500 0.031250 0.031250 0.000000 0.937500 0.000000 0.062500 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.062500 0.437500 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 0.906250 0.000000 0.093750 0.000000 0.000000 0.000000 1.000000 0.000000 0.968750 0.000000 0.031250 0.000000 0.781250 0.000000 0.218750 1.000000 0.000000 0.000000 0.000000 0.000000 0.906250 0.000000 0.093750 0.812500 0.187500 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.968750 0.031250 0.000000 0.000000 0.000000 0.968750 0.000000 0.031250 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 0.156250 0.000000 0.843750 0.000000 0.968750 0.000000 0.031250 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTAACAATCTTCCCWAAATCTCTCCACATTAACTACACGA MEME-1 regular expression -------------------------------------------------------------------------------- TTTAACAATCTTCCC[AT]AAATCTCTC[CT]ACATTAACTACACGA -------------------------------------------------------------------------------- Time 118.53 secs. ******************************************************************************** ******************************************************************************** MOTIF ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC MEME-2 width = 47 sites = 27 llr = 1474 E-value = 1.9e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9::aa9::::a:a1a:a::::a:a1:a1::aa::a::a:aaaa::a1 pos.-specific C ::a:::9a:9:::::::::::::::a:::::::::8::a:::::::9 probability G 11:::1::a::9:9::::::a:::8::1::::::::::::::::::: matrix T :9::::1::1:1:::a:aaa::a::::9aa::aa:29::::::aa:: bits 3.1 * * * * 2.8 * ** * * * 2.5 * *** * * * * * * 2.2 * **** * * * ** * * * Relative 1.9 * **** * * * ** * * * Entropy 1.5 * **** * * * ** * * * (78.7 bits) 1.2 ************************** ******** ********** 0.9 *************************** ******************* 0.6 *********************************************** 0.3 *********************************************** 0.0 ----------------------------------------------- Multilevel ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 47 n= 1094809 bayes= 15.108 E= 1.9e-044 122 -1140 -8 -1140 -1140 -1140 -66 127 -1140 304 -166 -1140 139 -1140 -1140 -1140 139 -1140 -1140 -1140 127 -1140 -66 -1140 -1140 292 -166 -237 -1140 304 -1140 -336 -1140 -1140 309 -1140 -1140 286 -1140 -137 133 -1140 -1140 -336 -1140 -1140 298 -237 139 -1140 -1140 -1140 -237 -1140 298 -1140 139 -1140 -1140 -1140 -1140 -166 -1140 133 139 -1140 -1140 -1140 -1140 -1140 -1140 139 -1140 -1140 -1140 139 -1140 -1140 -1140 139 -1140 -1140 309 -1140 139 -1140 -1140 -1140 -1140 -1140 -1140 139 139 -1140 -1140 -1140 -137 -166 280 -1140 -1140 309 -1140 -1140 133 -1140 -166 -1140 -237 -1140 -66 115 -336 -1140 -1140 133 -1140 -1140 -1140 139 139 -1140 -1140 -1140 139 -1140 -1140 -1140 -1140 -1140 -1140 139 -1140 -1140 -1140 139 139 -1140 -1140 -1140 -1140 280 -1140 -105 -336 -166 -1140 127 139 -1140 -1140 -1140 -1140 309 -1140 -1140 139 -1140 -1140 -1140 139 -1140 -1140 -1140 139 -1140 -1140 -1140 139 -1140 -1140 -1140 -1140 -1140 -1140 139 -1140 -1140 -1140 139 133 -1140 -1140 -336 -237 298 -1140 -1140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 47 nsites= 27 E= 1.9e-044 0.888889 0.000000 0.111111 0.000000 0.000000 0.000000 0.074074 0.925926 0.000000 0.962963 0.037037 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.925926 0.000000 0.074074 0.000000 0.000000 0.888889 0.037037 0.074074 0.000000 0.962963 0.000000 0.037037 0.000000 0.000000 1.000000 0.000000 0.000000 0.851852 0.000000 0.148148 0.962963 0.000000 0.000000 0.037037 0.000000 0.000000 0.925926 0.074074 1.000000 0.000000 0.000000 0.000000 0.074074 0.000000 0.925926 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.037037 0.000000 0.962963 1.000000 0.000000 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 0.000000 0.000000 1.000000 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 0.148148 0.037037 0.814815 0.000000 0.000000 1.000000 0.000000 0.000000 0.962963 0.000000 0.037037 0.000000 0.074074 0.000000 0.074074 0.851852 0.037037 0.000000 0.000000 0.962963 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.814815 0.000000 0.185185 0.037037 0.037037 0.000000 0.925926 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.962963 0.000000 0.000000 0.037037 0.074074 0.925926 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC MEME-2 regular expression -------------------------------------------------------------------------------- ATCAAACCGCAGAGATATTTGATAGCATTTAATTACTACAAAATTAC -------------------------------------------------------------------------------- Time 233.78 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************