******************************************************************************** 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/AT4G37260_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/AT4G37260_peak_sequences.fasta -dna -oc out/AT4G37260 -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= 1083 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= 190816 N= 1083 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.331 C 0.169 G 0.169 T 0.331 Background letter frequencies (from file dataset with add-one prior applied): A 0.333 C 0.167 G 0.167 T 0.333 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF ADTYAACSGWH MEME-1 width = 11 sites = 1080 llr = 7326 E-value = 2.1e-229 ******************************************************************************** -------------------------------------------------------------------------------- Motif ADTYAACSGWH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5321aa::134 pos.-specific C 1124::a3:13 probability G 14:::::58:: matrix T 2355:::1:64 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.5 *** * Entropy 1.3 *** * (9.8 bits) 1.0 ***** 0.8 ****** 0.5 ****** 0.3 ********** 0.0 ----------- Multilevel AGTTAACGGTA consensus TACC C AT sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ADTYAACSGWH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 179986 bayes= 8.03587 E= 2.1e-229 61 -24 -33 -61 -27 -71 112 -36 -90 46 -180 70 -256 128 -1672 69 158 -1672 -591 -1672 158 -491 -1672 -1672 -517 257 -1672 -1672 -517 89 168 -120 -122 -264 227 -390 -15 -58 -264 76 12 68 -417 12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ADTYAACSGWH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1080 E= 2.1e-229 0.506481 0.141667 0.133333 0.218519 0.275926 0.101852 0.362037 0.260185 0.178704 0.230556 0.048148 0.542593 0.056481 0.404630 0.000000 0.538889 0.997222 0.000000 0.002778 0.000000 0.994444 0.005556 0.000000 0.000000 0.009259 0.990741 0.000000 0.000000 0.009259 0.309259 0.537037 0.144444 0.142593 0.026852 0.808333 0.022222 0.299074 0.112037 0.026852 0.562037 0.362037 0.267593 0.009259 0.361111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ADTYAACSGWH MEME-1 regular expression -------------------------------------------------------------------------------- [AT][GAT][TC][TC]AAC[GC]G[TA][ATC] -------------------------------------------------------------------------------- Time 76.80 secs. ******************************************************************************** ******************************************************************************** MOTIF AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG MEME-2 width = 39 sites = 14 llr = 656 E-value = 1.6e-067 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9911::::::aa:1911:a:a9:11:9:::1:a::::1: pos.-specific C 1::::aa:::::::19::::::a::a::::9::1::::: probability G :191:::a:::::9:::a:::1:97:1:a1:1:::::9a matrix T :::9a:::aa::a:::9::a::::1::a:9:9:9aaa:: bits 2.6 *** * * * * * 2.3 *** * * * * * 2.1 *** * * ** * * ** 1.8 * *** * * * ** * * * ** Relative 1.5 * ********** * **** ** * ** * * ***** Entropy 1.3 * ************ ******* **** * ******* (67.6 bits) 1.0 *************************************** 0.8 *************************************** 0.5 *************************************** 0.3 *************************************** 0.0 --------------------------------------- Multilevel AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 149662 bayes= 14.6063 E= 1.6e-067 136 -23 -1045 -1045 136 -1045 -23 -1045 -122 -1045 236 -1045 -222 -1045 -122 136 -1045 -1045 -1045 159 -1045 258 -1045 -1045 -1045 258 -1045 -1045 -1045 -1045 258 -1045 -1045 -1045 -1045 159 -1045 -1045 -1045 159 159 -1045 -1045 -1045 159 -1045 -1045 -1045 -1045 -1045 -1045 159 -222 -1045 247 -1045 148 -122 -1045 -1045 -122 236 -1045 -1045 -122 -1045 -1045 136 -1045 -1045 258 -1045 159 -1045 -1045 -1045 -1045 -1045 -1045 159 159 -1045 -1045 -1045 148 -1045 -122 -1045 -1045 258 -1045 -1045 -222 -1045 247 -1045 -122 -1045 210 -122 -1045 258 -1045 -1045 148 -1045 -122 -1045 -1045 -1045 -1045 159 -1045 -1045 258 -1045 -1045 -1045 -23 136 -122 236 -1045 -1045 -1045 -1045 -23 136 159 -1045 -1045 -1045 -1045 -122 -1045 148 -1045 -1045 -1045 159 -1045 -1045 -1045 159 -1045 -1045 -1045 159 -222 -1045 247 -1045 -1045 -1045 258 -1045 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 14 E= 1.6e-067 0.857143 0.142857 0.000000 0.000000 0.857143 0.000000 0.142857 0.000000 0.142857 0.000000 0.857143 0.000000 0.071429 0.000000 0.071429 0.857143 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.071429 0.000000 0.928571 0.000000 0.928571 0.071429 0.000000 0.000000 0.142857 0.857143 0.000000 0.000000 0.142857 0.000000 0.000000 0.857143 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 0.928571 0.000000 0.071429 0.000000 0.000000 1.000000 0.000000 0.000000 0.071429 0.000000 0.928571 0.000000 0.142857 0.000000 0.714286 0.142857 0.000000 1.000000 0.000000 0.000000 0.928571 0.000000 0.071429 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.142857 0.857143 0.142857 0.857143 0.000000 0.000000 0.000000 0.000000 0.142857 0.857143 1.000000 0.000000 0.000000 0.000000 0.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG MEME-2 regular expression -------------------------------------------------------------------------------- AAGTTCCGTTAATGACTGATAACGGCATGTCTATTTTGG -------------------------------------------------------------------------------- Time 146.61 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************