******************************************************************************** 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/AT4G00730_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/AT4G00730_peak_sequences.fasta -dna -oc out/AT4G00730 -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= 6778 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= 1819816 N= 6778 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.38 C 0.12 G 0.12 T 0.38 Background letter frequencies (from file dataset with add-one prior applied): A 0.381 C 0.119 G 0.119 T 0.381 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTTCCCWAAATCTCTCCACATTAACTACACGATTAKTTACT MEME-1 width = 41 sites = 22 llr = 1138 E-value = 1.9e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTCCCWAAATCTCTCCACATTAACTACACGATTAKTTACT MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::::6aaa:::::::a:a::aa::a:a::a::a:::a:: pos.-specific C a::aa9:::::a:a:a9:a:::::a::a:a:::::::::9: probability G ::::::::::::::::::::::::::::::a::::6::::: matrix T :aa::14:::a:a:a:1:::aa:::a::::::aa:3aa::a bits 3.1 * * * * 2.8 * ** * * * * * * ** 2.5 * ** * * ** * * * ** * 2.1 * *** * * ** * * * ** * Relative 1.8 * *** * * ** * * * ** * Entropy 1.5 ****** *************************** ** ** (74.6 bits) 1.2 ****** ********************************** 0.9 ****** ********************************** 0.6 ****** ********************************** 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel CTTCCCAAAATCTCTCCACATTAACTACACGATTAGTTACT consensus T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCCCWAAATCTCTCCACATTAACTACACGATTAKTTACT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 1548696 bayes= 17.6366 E= 1.9e-010 -306 300 -1110 -1110 -1110 -1110 -1110 139 -1110 -1110 -1110 139 -1110 300 -1110 -306 -1110 307 -1110 -1110 -1110 285 -1110 -148 74 -1110 -1110 -7 139 -1110 -1110 -1110 139 -1110 -1110 -1110 139 -1110 -1110 -1110 -1110 -1110 -1110 139 -306 300 -1110 -1110 -1110 -1110 -1110 139 -1110 307 -1110 -1110 -1110 -1110 -1110 139 -1110 300 -1110 -306 -1110 293 -1110 -206 139 -1110 -1110 -1110 -1110 300 -1110 -306 139 -1110 -1110 -1110 -1110 -1110 -1110 139 -1110 -1110 -1110 139 139 -1110 -1110 -1110 139 -1110 -1110 -1110 -1110 300 -1110 -306 -1110 -1110 -1110 139 139 -1110 -1110 -1110 -1110 307 -1110 -1110 139 -1110 -1110 -1110 -1110 307 -1110 -1110 -306 -1110 300 -1110 139 -1110 -1110 -1110 -1110 -1110 -1110 139 -1110 -1110 -1110 139 133 -1110 -139 -1110 -306 -1110 241 -26 -1110 -1110 -1110 139 -1110 -1110 -1110 139 133 -1110 -1110 -306 -306 293 -1110 -306 -1110 -1110 -1110 139 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCCCWAAATCTCTCCACATTAACTACACGATTAKTTACT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 22 E= 1.9e-010 0.045455 0.954545 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.954545 0.000000 0.045455 0.000000 1.000000 0.000000 0.000000 0.000000 0.863636 0.000000 0.136364 0.636364 0.000000 0.000000 0.363636 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 0.045455 0.954545 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 0.954545 0.000000 0.045455 0.000000 0.909091 0.000000 0.090909 1.000000 0.000000 0.000000 0.000000 0.000000 0.954545 0.000000 0.045455 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.954545 0.000000 0.045455 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 0.045455 0.000000 0.954545 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 0.954545 0.000000 0.045455 0.000000 0.045455 0.000000 0.636364 0.318182 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.954545 0.000000 0.000000 0.045455 0.045455 0.909091 0.000000 0.045455 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTCCCWAAATCTCTCCACATTAACTACACGATTAKTTACT MEME-1 regular expression -------------------------------------------------------------------------------- CTTCCC[AT]AAATCTCTCCACATTAACTACACGATTA[GT]TTACT -------------------------------------------------------------------------------- Time 79.55 secs. ******************************************************************************** ******************************************************************************** MOTIF WDYAATWAATR MEME-2 width = 11 sites = 6695 llr = 41729 E-value = 2.9e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif WDYAATWAATR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 44288:3aa:3 pos.-specific C 2132::::::: probability G 23::::::::5 matrix T 225:2a7::a2 bits 3.1 2.8 2.5 2.1 Relative 1.8 Entropy 1.5 * (9.0 bits) 1.2 * *** 0.9 * * **** 0.6 *** **** 0.3 ********** 0.0 ----------- Multilevel AATAATTAATG consensus TGC T A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WDYAATWAATR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1752036 bayes= 10.067 E= 2.9e-008 15 72 39 -76 -2 24 126 -95 -123 127 -484 52 111 55 -500 -1935 105 -1935 -1935 -85 -1935 -964 -584 139 -17 -345 -1935 77 139 -1935 -1935 -1935 136 -1935 -1935 -425 -1131 -1935 -425 138 -31 -1935 216 -124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WDYAATWAATR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6695 E= 2.9e-008 0.421060 0.197311 0.156684 0.224944 0.375205 0.141150 0.286184 0.197461 0.162509 0.288275 0.004182 0.545034 0.821509 0.174757 0.003734 0.000000 0.789544 0.000000 0.000000 0.210456 0.000000 0.000149 0.002091 0.997760 0.337864 0.010904 0.000000 0.651232 1.000000 0.000000 0.000000 0.000000 0.979985 0.000000 0.000000 0.020015 0.000149 0.000000 0.006273 0.993577 0.307095 0.000000 0.531889 0.161016 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WDYAATWAATR MEME-2 regular expression -------------------------------------------------------------------------------- [AT][AG][TC]A[AT]T[TA]AAT[GA] -------------------------------------------------------------------------------- Time 150.04 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************