******************************************************************************** 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/AT5G58850_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/AT5G58850_peak_sequences.fasta -dna -oc out/AT5G58850 -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= 5406 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= 1142283 N= 5406 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.33 C 0.17 G 0.17 T 0.33 Background letter frequencies (from file dataset with add-one prior applied): A 0.332 C 0.168 G 0.168 T 0.332 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YGTAACGKHHR MEME-1 width = 11 sites = 5379 llr = 42131 E-value = 5.1e-372 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGTAACGKHHR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 231aa:::434 pos.-specific C 2::::a11231 probability G 17::::86::2 matrix T 4:9:::13452 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.5 **** Entropy 1.3 * **** (11.3 bits) 1.0 ******* 0.8 ******* 0.5 ******* 0.3 ********* 0.0 ----------- Multilevel TGTAACGGATA consensus CA TTCG sequence A CAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTAACGKHHR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1088223 bayes= 9.72924 E= 5.1e-372 -59 57 -103 43 -40 -465 212 -469 -144 -1904 -1904 140 159 -1904 -1904 -1904 159 -1904 -1904 -1904 -1904 257 -1904 -1904 -689 -23 224 -248 -848 -91 175 5 28 33 -446 19 -36 67 -289 44 35 -29 50 -71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTAACGKHHR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5379 E= 5.1e-372 0.221231 0.249303 0.082543 0.446923 0.251534 0.006693 0.728946 0.012828 0.122699 0.000000 0.000000 0.877301 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.002789 0.143335 0.794200 0.059677 0.000930 0.089236 0.566462 0.343372 0.403049 0.210634 0.007622 0.378695 0.259156 0.266778 0.022681 0.451385 0.423313 0.137386 0.237033 0.202268 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTAACGKHHR MEME-1 regular expression -------------------------------------------------------------------------------- [TCA][GA]TAACG[GT][ATC][TCA][AGT] -------------------------------------------------------------------------------- Time 73.95 secs. ******************************************************************************** ******************************************************************************** MOTIF MRAARAARAARAARAARAARA MEME-2 width = 21 sites = 1086 llr = 10865 E-value = 1.9e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif MRAARAARAARAARAARAARA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 457846868948767869745 pos.-specific C 2::1222::1111:11:::22 probability G 243132:42:5:231141232 matrix T 21::111:::::::1:::111 bits 2.6 2.3 2.1 1.8 Relative 1.5 Entropy 1.3 (14.4 bits) 1.0 *** * * *** 0.8 ** **** *** *** 0.5 *** ************* 0.3 ******************** 0.0 --------------------- Multilevel AAAAAAAAAAGAAAAAAAAAA consensus CGG G GG A G G GC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MRAARAARAARAARAARAARA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1034163 bayes= 12.0561 E= 1.9e-024 29 42 9 -80 62 -334 123 -207 102 -190 69 -517 128 -114 -81 -379 39 7 82 -188 79 22 3 -249 119 12 -1673 -245 87 -1673 120 -503 122 -1673 36 -503 139 -125 -293 -325 19 -84 153 -303 136 -73 -1673 -277 114 -69 -2 -1673 95 -342 104 -1673 117 -31 -132 -271 132 -142 -59 -1673 88 -1673 119 -591 136 -215 -64 -1673 114 -281 3 -215 43 8 93 -254 67 30 30 -245 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MRAARAARAARAARAARAARA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1086 E= 1.9e-024 0.406077 0.224678 0.178637 0.190608 0.511050 0.016575 0.393186 0.079190 0.674954 0.045120 0.270718 0.009208 0.803867 0.076427 0.095764 0.023941 0.435543 0.176796 0.297422 0.090239 0.573665 0.195212 0.172192 0.058932 0.755985 0.183241 0.000000 0.060773 0.604972 0.000000 0.384899 0.010129 0.774401 0.000000 0.215470 0.010129 0.872007 0.070902 0.022099 0.034991 0.378453 0.093923 0.487109 0.040516 0.849908 0.101289 0.000000 0.048803 0.730203 0.104052 0.165746 0.000000 0.639042 0.015654 0.345304 0.000000 0.746777 0.135359 0.067219 0.050645 0.825967 0.062615 0.111418 0.000000 0.610497 0.000000 0.383978 0.005525 0.854512 0.037753 0.107735 0.000000 0.729282 0.023941 0.172192 0.074586 0.445672 0.177716 0.319521 0.057090 0.526703 0.206262 0.206262 0.060773 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MRAARAARAARAARAARAARA MEME-2 regular expression -------------------------------------------------------------------------------- [AC][AG][AG]A[AG]AA[AG][AG]A[GA]AA[AG]AA[AG]AA[AG][ACG] -------------------------------------------------------------------------------- Time 141.25 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************