******************************************************************************** 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/AT3G50410_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/AT3G50410_peak_sequences.fasta -dna -oc out/AT3G50410 -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= 6420 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= 1534252 N= 6420 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.36 C 0.14 G 0.14 T 0.36 Background letter frequencies (from file dataset with add-one prior applied): A 0.36 C 0.14 G 0.14 T 0.36 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAAAAAAAAAAAAG MEME-1 width = 15 sites = 6417 llr = 48202 E-value = 6.7e-248 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 667897766798a92 pos.-specific C 1111:11111::::1 probability G 2212122322:2:17 matrix T 111::1111:1:::: bits 2.8 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 * * (10.8 bits) 1.1 **** 0.9 * ***** 0.6 ***** ****** 0.3 *************** 0.0 --------------- Multilevel AAAAAAAAAAAAAAG consensus G GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1444372 bayes= 9.79701 E= 6.7e-248 74 -33 14 -144 68 -43 70 -197 97 -26 -49 -224 106 -110 26 -439 127 -226 -51 -601 98 -142 41 -283 97 -119 11 -212 61 -107 85 -146 73 -56 69 -215 94 -93 51 -324 133 -405 -581 -215 124 -1929 11 -1929 145 -354 -1929 -701 134 -1929 -71 -1929 -100 -124 239 -358 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6417 E= 6.7e-248 0.601839 0.111267 0.154122 0.132772 0.577684 0.103475 0.226586 0.092255 0.707807 0.116410 0.099423 0.076360 0.750195 0.065139 0.167524 0.017142 0.867384 0.029141 0.097865 0.005610 0.711236 0.052205 0.185912 0.050647 0.705314 0.060932 0.150693 0.083061 0.551036 0.066230 0.251675 0.131058 0.599345 0.094592 0.224871 0.081191 0.689730 0.073243 0.199003 0.038024 0.907589 0.008415 0.002493 0.081502 0.849462 0.000000 0.150538 0.000000 0.985196 0.011999 0.000000 0.002805 0.914914 0.000000 0.085086 0.000000 0.179679 0.059218 0.731027 0.030076 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 regular expression -------------------------------------------------------------------------------- A[AG]AAAAA[AG][AG]AAAAAG -------------------------------------------------------------------------------- Time 66.96 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAAAGTAAAA MEME-2 width = 11 sites = 6412 llr = 42011 E-value = 6.7e-089 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAGTAAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 79aaa:25766 pos.-specific C 1:::::11:11 probability G 1::::a22211 matrix T 11::::52112 bits 2.8 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.5 bits) 1.1 **** 0.9 ***** 0.6 ***** * 0.3 ****** ** 0.0 ----------- Multilevel AAAAAGTAAAA consensus AT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGTAAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1470052 bayes= 9.82335 E= 6.7e-089 94 -18 -61 -197 132 -516 -476 -195 147 -1929 -880 -1929 146 -780 -505 -1117 147 -1929 -648 -1929 -502 -610 282 -1929 -81 -15 52 37 56 -78 25 -70 92 -214 41 -183 77 -24 -15 -133 61 -20 -4 -91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGTAAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6412 E= 6.7e-089 0.693699 0.123206 0.091235 0.091859 0.897380 0.003899 0.005147 0.093575 0.999688 0.000000 0.000312 0.000000 0.995009 0.000624 0.004211 0.000156 0.998440 0.000000 0.001560 0.000000 0.011073 0.002027 0.986900 0.000000 0.206176 0.125858 0.200717 0.467249 0.532127 0.081098 0.165627 0.221148 0.681847 0.031659 0.185122 0.101372 0.612913 0.118216 0.125546 0.143325 0.551622 0.121179 0.135371 0.191828 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGTAAAA MEME-2 regular expression -------------------------------------------------------------------------------- AAAAAG[TAG][AT]AAA -------------------------------------------------------------------------------- Time 128.75 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************