******************************************************************************** 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/AT3G09600_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/AT3G09600_peak_sequences.fasta -dna -oc out/AT3G09600 -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= 11045 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= 2944565 N= 11045 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.365 C 0.135 G 0.135 T 0.365 Background letter frequencies (from file dataset with add-one prior applied): A 0.366 C 0.134 G 0.134 T 0.366 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAAAAAWATCT MEME-1 width = 11 sites = 11020 llr = 80592 E-value = 1.3e-163 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAAAAAWATCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4579aa4a::2 pos.-specific C 211::::::a1 probability G 221:::::::: matrix T 2221::6:a:6 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 ** *** (10.6 bits) 1.2 ** *** 0.9 *** *** 0.6 ******* 0.3 ********** 0.0 ----------- Multilevel AAAAAATATCT consensus T A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAAAAWATCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2834113 bayes= 10.1991 E= 1.3e-163 24 40 28 -68 59 -15 17 -103 85 -55 -69 -112 127 -365 -412 -186 142 -337 -416 -1097 145 -589 -2007 -1039 9 -2007 -416 72 145 -953 -2007 -1197 -2007 -2007 -2007 145 -2007 290 -2007 -2007 -58 -10 -287 74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAAAAWATCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 11020 E= 1.3e-163 0.431488 0.177586 0.162523 0.228403 0.549183 0.121325 0.150817 0.178675 0.657441 0.091833 0.082940 0.167786 0.880853 0.010708 0.007713 0.100726 0.979310 0.012976 0.007532 0.000181 0.997459 0.002269 0.000000 0.000272 0.388748 0.000000 0.007532 0.603721 0.999728 0.000181 0.000000 0.000091 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.244374 0.125590 0.018330 0.611706 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAAAAWATCT MEME-1 regular expression -------------------------------------------------------------------------------- [AT]AAAAA[TA]ATC[TA] -------------------------------------------------------------------------------- Time 71.80 secs. ******************************************************************************** ******************************************************************************** MOTIF YYCAACTACAGGATTTATTTCACAAAATGGCTGCAAAAATG MEME-2 width = 41 sites = 44 llr = 1838 E-value = 1.3e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYCAACTACAGGATTTATTTCACAAAATGGCTGCAAAAATG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::aa::5:a21a:::a::::9:aaa8:22::::aaaaa:2 pos.-specific C 658::8:36:::::::::::818:::::::8::a::::::: probability G :::::1::2:69::::::::1:::::2:88::a:::::::8 matrix T 441:::a12:2::aaa:aaa1:2::::a::1a:::::::a: bits 2.9 2.6 ** 2.3 ** 2.0 * * * ** ** Relative 1.7 * * * * * *** ** * Entropy 1.4 ***** * ** * * ** **** **** ****** * (60.3 bits) 1.2 ******* ** ****************************** 0.9 ******* ********************************* 0.6 ******* ********************************* 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel CCCAACTACAGGATTTATTTCACAAAATGGCTGCAAAAATG consensus TT C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYCAACTACAGGATTTATTTCACAAAATGGCTGCAAAAATG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 2502763 bayes= 17.8766 E= 1.3e-004 -1210 208 -156 8 -301 202 -1210 16 -1210 265 -256 -142 142 -256 -1210 -1210 145 -1210 -1210 -1210 -301 261 -56 -301 -1210 -1210 -256 142 58 102 -156 -142 -400 225 25 -101 145 -1210 -1210 -1210 -84 -256 214 -101 -201 -1210 272 -400 145 -1210 -1210 -1210 -400 -256 -1210 138 -1210 -1210 -1210 145 -400 -1210 -1210 142 145 -1210 -1210 -1210 -1210 -256 -256 138 -400 -1210 -1210 142 -1210 -1210 -1210 145 -400 253 -56 -169 131 -98 -1210 -400 -1210 261 -1210 -101 145 -1210 -1210 -1210 145 -1210 -1210 -1210 145 -1210 -1210 -1210 120 -1210 25 -1210 -1210 -1210 -1210 145 -101 -1210 257 -400 -120 -1210 265 -1210 -400 265 -1210 -142 -400 -1210 -256 138 -400 -1210 286 -1210 -400 283 -1210 -400 145 -1210 -1210 -1210 145 -1210 -1210 -1210 145 -1210 -1210 -1210 142 -1210 -256 -1210 142 -1210 -1210 -400 -400 -1210 -256 138 -120 -1210 257 -301 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYCAACTACAGGATTTATTTCACAAAATGGCTGCAAAAATG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 44 E= 1.3e-004 0.000000 0.568182 0.045455 0.386364 0.045455 0.545455 0.000000 0.409091 0.000000 0.840909 0.022727 0.136364 0.977273 0.022727 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.045455 0.818182 0.090909 0.045455 0.000000 0.000000 0.022727 0.977273 0.545455 0.272727 0.045455 0.136364 0.022727 0.636364 0.159091 0.181818 1.000000 0.000000 0.000000 0.000000 0.204545 0.022727 0.590909 0.181818 0.090909 0.000000 0.886364 0.022727 1.000000 0.000000 0.000000 0.000000 0.022727 0.022727 0.000000 0.954545 0.000000 0.000000 0.000000 1.000000 0.022727 0.000000 0.000000 0.977273 1.000000 0.000000 0.000000 0.000000 0.000000 0.022727 0.022727 0.954545 0.022727 0.000000 0.000000 0.977273 0.000000 0.000000 0.000000 1.000000 0.022727 0.772727 0.090909 0.113636 0.909091 0.068182 0.000000 0.022727 0.000000 0.818182 0.000000 0.181818 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.840909 0.000000 0.159091 0.000000 0.000000 0.000000 0.000000 1.000000 0.181818 0.000000 0.795455 0.022727 0.159091 0.000000 0.840909 0.000000 0.022727 0.840909 0.000000 0.136364 0.022727 0.000000 0.022727 0.954545 0.022727 0.000000 0.977273 0.000000 0.022727 0.954545 0.000000 0.022727 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.977273 0.000000 0.022727 0.000000 0.977273 0.000000 0.000000 0.022727 0.022727 0.000000 0.022727 0.954545 0.159091 0.000000 0.795455 0.045455 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYCAACTACAGGATTTATTTCACAAAATGGCTGCAAAAATG MEME-2 regular expression -------------------------------------------------------------------------------- [CT][CT]CAACT[AC]CA[GA]GATTTATTTCACAAAATGGCTGCAAAAATG -------------------------------------------------------------------------------- Time 138.95 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************