******************************************************************************** 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/AT5G56840_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/AT5G56840_peak_sequences.fasta -dna -oc out/AT5G56840 -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= 5053 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= 1126013 N= 5053 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.357 C 0.143 G 0.143 T 0.357 Background letter frequencies (from file dataset with add-one prior applied): A 0.358 C 0.142 G 0.142 T 0.358 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWTGGATAARRWW MEME-1 width = 13 sites = 5051 llr = 38371 E-value = 1.1e-259 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWTGGATAARRWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4423:a:a93433 pos.-specific C :11::::::1111 probability G :2:7a:::14411 matrix T 546:::a:12155 bits 2.8 * 2.5 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (11.0 bits) 1.1 ***** 0.8 ****** 0.6 ****** * 0.3 * ********* 0.0 ------------- Multilevel TATGGATAAGGTT consensus ATAA AAAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTGGATAARRWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 1065377 bayes= 9.90171 E= 1.1e-259 20 -237 -198 56 9 -110 29 9 -63 -66 -179 84 -18 -849 226 -882 -982 -1895 281 -1081 148 -1895 -1895 -1081 -923 -1895 -1895 148 142 -1895 -503 -319 133 -1895 -148 -283 -49 -47 166 -88 18 -80 157 -195 -31 -19 -89 51 -14 -49 -35 37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTGGATAARRWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 5051 E= 1.1e-259 0.410810 0.027519 0.036032 0.525638 0.379529 0.066521 0.174421 0.379529 0.230449 0.090081 0.041180 0.638289 0.316571 0.000396 0.682241 0.000792 0.000396 0.000000 0.999406 0.000198 0.999802 0.000000 0.000000 0.000198 0.000594 0.000000 0.000000 0.999406 0.956444 0.000000 0.004356 0.039200 0.898832 0.000000 0.050881 0.050287 0.254603 0.102752 0.448426 0.194219 0.404276 0.081766 0.421501 0.092457 0.289448 0.124530 0.076618 0.509404 0.323698 0.101168 0.111859 0.463275 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWTGGATAARRWW MEME-1 regular expression -------------------------------------------------------------------------------- [TA][AT][TA][GA]GATAA[GA][GA][TA][TA] -------------------------------------------------------------------------------- Time 75.41 secs. ******************************************************************************** ******************************************************************************** MOTIF CGCCTAAATAGGCGGGTGTAAGATGTAACTGTAATTTTTTATCGATAATA MEME-2 width = 50 sites = 4 llr = 256 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGCCTAAATAGGCGGGTGTAAGATGTAACTGTAATTTTTTATCGATAATA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::aaa:a:::3:::::aa:a:3:aa::::a8::::::a:::a:aa:a pos.-specific C a:aa::::::::a:::3::::3::::::a:::::::::::::a::::::: probability G :a::::::::aa:8aa:a:::8::8:::::a::::::::::::a:::::: matrix T ::::a:::a:::::::8:a::::a:a:::a:a:3aaaaaa:a:::a::a: bits 2.8 **** *** ** * * * ** 2.5 **** *** ** * * * ** 2.3 **** *** ** * * * ** 2.0 **** *** ** * * * * ** Relative 1.7 **** ****** * * * * * ** Entropy 1.4 **************** **************** **************** (92.4 bits) 1.1 ********************************* **************** 0.8 ********************************* **************** 0.6 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel CGCCTAAATAGGCGGGTGTAAGATGTAACTGTAATTTTTTATCGATAATA consensus A C C A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTAAATAGGCGGGTGTAAGATGTAACTGTAATTTTTTATCGATAATA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 878416 bayes= 17.7445 E= 1.5e-004 -865 281 -865 -865 -865 -865 281 -865 -865 281 -865 -865 -865 281 -865 -865 -865 -865 -865 148 148 -865 -865 -865 148 -865 -865 -865 148 -865 -865 -865 -865 -865 -865 148 148 -865 -865 -865 -865 -865 281 -865 -865 -865 281 -865 -865 281 -865 -865 -52 -865 240 -865 -865 -865 281 -865 -865 -865 281 -865 -865 81 -865 107 -865 -865 281 -865 -865 -865 -865 148 148 -865 -865 -865 148 -865 -865 -865 -865 81 240 -865 148 -865 -865 -865 -865 -865 -865 148 -52 -865 240 -865 -865 -865 -865 148 148 -865 -865 -865 148 -865 -865 -865 -865 281 -865 -865 -865 -865 -865 148 -865 -865 281 -865 -865 -865 -865 148 148 -865 -865 -865 107 -865 -865 -52 -865 -865 -865 148 -865 -865 -865 148 -865 -865 -865 148 -865 -865 -865 148 -865 -865 -865 148 -865 -865 -865 148 148 -865 -865 -865 -865 -865 -865 148 -865 281 -865 -865 -865 -865 281 -865 148 -865 -865 -865 -865 -865 -865 148 148 -865 -865 -865 148 -865 -865 -865 -865 -865 -865 148 148 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTAAATAGGCGGGTGTAAGATGTAACTGTAATTTTTTATCGATAATA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 4 E= 1.5e-004 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 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 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.750000 0.000000 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 1.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.000000 0.250000 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 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 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 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 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGCCTAAATAGGCGGGTGTAAGATGTAACTGTAATTTTTTATCGATAATA MEME-2 regular expression -------------------------------------------------------------------------------- CGCCTAAATAGGC[GA]GG[TC]GTAA[GC]AT[GA]TAACTGTA[AT]TTTTTTATCGATAATA -------------------------------------------------------------------------------- Time 142.64 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************