******************************************************************************** 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/AT2G30250_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/AT2G30250_peak_sequences.fasta -dna -oc out/AT2G30250 -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= 5596 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= 1068151 N= 5596 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.333 C 0.167 G 0.167 T 0.333 Background letter frequencies (from file dataset with add-one prior applied): A 0.335 C 0.165 G 0.165 T 0.335 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWWRGTCAAMR MEME-1 width = 11 sites = 5456 llr = 45776 E-value = 7.3e-525 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWWRGTCAAMR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4556:::aa43 pos.-specific C 211:::a::52 probability G 1114a:::::4 matrix T 334::a:::11 bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * Relative 1.6 ***** Entropy 1.3 ***** (12.1 bits) 1.0 ****** 0.8 ******* 0.5 ******* 0.3 ******** 0.0 ----------- Multilevel AAAAGTCAACG consensus TTTG AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWRGTCAAMR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1012191 bayes= 9.78957 E= 7.3e-525 40 1 -56 -26 58 -32 -109 -22 45 -79 -89 9 87 -469 118 -598 -1906 -1906 259 -519 -1906 -1906 -1906 158 -1906 260 -1906 -1906 158 -1906 -1906 -1906 157 -1906 -491 -1906 32 166 -1906 -246 -36 16 132 -122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWRGTCAAMR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5456 E= 7.3e-525 0.441532 0.166606 0.112353 0.279509 0.501650 0.132331 0.077713 0.288306 0.458394 0.095674 0.089076 0.356855 0.613453 0.006415 0.374817 0.005315 0.000000 0.000000 0.990836 0.009164 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.994501 0.000000 0.005499 0.000000 0.416789 0.522177 0.000000 0.061034 0.260264 0.184934 0.411474 0.143328 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWRGTCAAMR MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][AT][AG]GTCAA[CA][GA] -------------------------------------------------------------------------------- Time 152.26 secs. ******************************************************************************** ******************************************************************************** Stopped because MEME would probably exceed the allowed time (300.00 secs) before finding the next motif. ******************************************************************************** CPU: nid004083 ********************************************************************************