******************************************************************************** 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/AT1G47655_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/AT1G47655_peak_sequences.fasta -dna -oc out/AT1G47655 -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= 6251 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= 1527441 N= 6251 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.362 C 0.138 G 0.138 T 0.362 Background letter frequencies (from file dataset with add-one prior applied): A 0.362 C 0.138 G 0.138 T 0.362 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTTTTTTTTTTTWCTTTTTB MEME-1 width = 21 sites = 6247 llr = 48506 E-value = 7.6e-272 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTTTTTTTTTTWCTTTTTB MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2221111111::13::::112 pos.-specific C 2222122221121181:1:13 probability G 11111:111:1:111::::12 matrix T 556677666788751999984 bits 2.9 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 * (11.2 bits) 1.1 * ** 0.9 ***** 0.6 * *** ****** 0.3 ************* ******* 0.0 --------------------- Multilevel TTTTTTTTTTTTTTCTTTTTT consensus CC C A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTTTTTTTWCTTTTTB MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1402421 bayes= 9.796 E= 7.6e-272 -112 55 -7 47 -114 64 -64 55 -109 20 -105 74 -148 41 -69 73 -162 -14 -118 94 -180 50 -226 89 -136 16 -71 78 -154 21 -29 74 -194 82 -101 71 -171 -18 -189 101 -365 -26 -124 114 -369 31 -182 107 -160 -8 -126 93 -17 -75 -55 47 -413 248 -89 -143 -358 -82 -1925 130 -541 -234 -192 136 -1925 -49 -1925 132 -279 -197 -164 126 -279 -46 -107 111 -110 99 51 -1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTTTTTTTWCTTTTTB MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6247 E= 7.6e-272 0.166000 0.201537 0.131583 0.500880 0.164079 0.215623 0.088843 0.531455 0.169521 0.158476 0.066912 0.605090 0.129662 0.183928 0.085321 0.601089 0.117977 0.125020 0.060829 0.696174 0.103570 0.194653 0.028814 0.672963 0.140547 0.154634 0.084200 0.620618 0.124060 0.159276 0.112694 0.603970 0.094445 0.244597 0.068513 0.592444 0.110293 0.122299 0.037138 0.730271 0.028814 0.115415 0.058268 0.797503 0.028013 0.170962 0.039219 0.761806 0.119577 0.130943 0.057788 0.691692 0.322075 0.082119 0.094605 0.501201 0.020650 0.770290 0.074756 0.134304 0.030255 0.078117 0.000000 0.891628 0.008484 0.027213 0.036498 0.927805 0.000000 0.098127 0.000000 0.901873 0.052185 0.035217 0.044341 0.868257 0.052185 0.100208 0.065792 0.781815 0.168561 0.274372 0.197215 0.359853 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTTTTTTTTTWCTTTTTB MEME-1 regular expression -------------------------------------------------------------------------------- [TC][TC]TTTTTT[TC]TTTT[TA]CTTTTT[TC] -------------------------------------------------------------------------------- Time 120.39 secs. ******************************************************************************** ******************************************************************************** MOTIF MCTTTTTB MEME-2 width = 8 sites = 5928 llr = 39042 E-value = 5.3e-027 ******************************************************************************** -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4::::1:1 pos.-specific C 2a::::12 probability G 1:::::13 matrix T 2:aaa984 bits 2.9 * 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 ACTTTTTT consensus C G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1483684 bayes= 10.0581 E= 5.3e-027 29 74 12 -102 -1918 284 -1918 -466 -1918 -1918 -1918 147 -1918 -1918 -1918 147 -1918 -1918 -1918 147 -228 -1918 -1918 135 -1918 -126 -47 122 -155 70 94 10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 5928 E= 5.3e-027 0.441127 0.230094 0.149798 0.178981 0.000000 0.985661 0.000000 0.014339 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.074561 0.000000 0.000000 0.925439 0.000000 0.057692 0.099696 0.842611 0.123819 0.223853 0.265520 0.386808 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 regular expression -------------------------------------------------------------------------------- [AC]CTTTTT[TGC] -------------------------------------------------------------------------------- Time 228.23 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************