******************************************************************************** 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/AT3G16280_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/AT3G16280_peak_sequences.fasta -dna -oc out/AT3G16280 -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= 3345 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= 666917 N= 3345 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.292 C 0.208 G 0.208 T 0.292 Background letter frequencies (from file dataset with add-one prior applied): A 0.294 C 0.206 G 0.206 T 0.294 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGTCGGTGRND MEME-1 width = 11 sites = 3253 llr = 29630 E-value = 4.0e-641 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTCGGTGRND MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::::::2433 pos.-specific C 2::a::31131 probability G :a1:aa:6423 matrix T 7:9:::72133 bits 2.3 * *** 2.1 * *** 1.8 * *** 1.6 * *** Relative 1.4 ***** Entropy 1.1 ****** (13.1 bits) 0.9 ******* 0.7 ******* 0.5 ******** 0.2 ********* 0.0 ----------- Multilevel TGTCGGTGGAG consensus C C ATA sequence CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTCGGTGRND MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 633467 bayes= 9.92225 E= 4.0e-641 -295 14 -1831 132 -990 -1831 228 -1831 -351 -1831 -198 165 -1831 228 -1831 -1831 -1831 -1831 228 -1831 -990 -1831 228 -1831 -990 60 -1831 123 -88 -119 152 -89 34 -82 87 -112 4 29 -40 -1 -1 -72 53 -4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTCGGTGRND MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 3253 E= 4.0e-641 0.038119 0.227482 0.000000 0.734399 0.000307 0.000000 0.999693 0.000000 0.025822 0.000000 0.052259 0.921918 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000307 0.000000 0.999693 0.000000 0.000307 0.311405 0.000000 0.688288 0.160160 0.090071 0.590532 0.159238 0.371657 0.116200 0.376575 0.135567 0.301568 0.250845 0.155856 0.291731 0.291423 0.124808 0.297571 0.286197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTCGGTGRND MEME-1 regular expression -------------------------------------------------------------------------------- [TC]GTCGG[TC]G[GA][ATC][GAT] -------------------------------------------------------------------------------- Time 79.92 secs. ******************************************************************************** ******************************************************************************** MOTIF YCTYCWYCDYCKYCK MEME-2 width = 15 sites = 864 llr = 8914 E-value = 3.8e-087 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCTYCWYCDYCKYCK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:2::3::2::1::2 pos.-specific C 48158:5a:6a:59: probability G 1:21:2::3::5::4 matrix T 5154155:54:4513 bits 2.3 * * 2.1 * * 1.8 * * 1.6 * * * Relative 1.4 * * * * * Entropy 1.1 * * * * ** (14.9 bits) 0.9 * ** ** ** ** 0.7 * ** ** ** ** 0.5 ** ** ******** 0.2 *************** 0.0 --------------- Multilevel TCTCCTTCTCCGCCG consensus C AT AC GT TT T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTYCWYCDYCKYCK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 620087 bayes= 11.7056 E= 3.8e-087 -211 93 -134 64 -367 203 -1640 -108 -32 -162 -13 79 -1640 135 -183 51 -353 202 -547 -114 -13 -247 -5 75 -340 121 -1640 76 -1640 228 -1640 -1640 -32 -1640 56 64 -518 154 -447 38 -1640 228 -1640 -1640 -104 -339 121 30 -1640 139 -1640 64 -1640 213 -339 -190 -70 -243 110 21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTYCWYCDYCKYCK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 864 E= 3.8e-087 0.068287 0.391204 0.081019 0.459491 0.023148 0.837963 0.000000 0.138889 0.236111 0.067130 0.187500 0.509259 0.000000 0.523148 0.057870 0.418981 0.025463 0.836806 0.004630 0.133102 0.269676 0.037037 0.199074 0.494213 0.027778 0.474537 0.000000 0.497685 0.000000 1.000000 0.000000 0.000000 0.236111 0.000000 0.304398 0.459491 0.008102 0.599537 0.009259 0.383102 0.000000 1.000000 0.000000 0.000000 0.143519 0.019676 0.475694 0.361111 0.000000 0.540509 0.000000 0.459491 0.000000 0.901620 0.019676 0.078704 0.181713 0.038194 0.439815 0.340278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCTYCWYCDYCKYCK MEME-2 regular expression -------------------------------------------------------------------------------- [TC]C[TA][CT]C[TA][TC]C[TGA][CT]C[GT][CT]C[GT] -------------------------------------------------------------------------------- Time 149.28 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************