******************************************************************************** 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/AT3G50260_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/AT3G50260_peak_sequences.fasta -dna -oc out/AT3G50260 -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= 5348 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= 1023198 N= 5348 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.28 C 0.22 G 0.22 T 0.28 Background letter frequencies (from file dataset with add-one prior applied): A 0.282 C 0.218 G 0.218 T 0.282 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HDDTGTCGGTGRHD MEME-1 width = 14 sites = 5273 llr = 44967 E-value = 1.9e-519 ******************************************************************************** -------------------------------------------------------------------------------- Motif HDDTGTCGGTGRHD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3331:2::::1333 pos.-specific C 2112::a::21121 probability G 1332a1:aa:7413 matrix T 3345:7:::81133 bits 2.2 * *** 2.0 * *** 1.8 * *** 1.5 * *** Relative 1.3 * **** Entropy 1.1 * **** (12.3 bits) 0.9 * ***** 0.7 ******* 0.4 ******* 0.2 ********** 0.0 -------------- Multilevel TTTTGTCGGTGGTG consensus AAAG AAT sequence CGG CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDTGTCGGTGRHD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 953674 bayes= 9.68521 E= 1.9e-519 0 17 -74 28 -1 -77 24 24 6 -159 20 44 -165 -36 7 86 -1901 -1901 220 -1901 -78 -449 -85 132 -1901 220 -1901 -1901 -1901 -1901 220 -1901 -1901 -1901 220 -1901 -1901 -37 -1901 156 -216 -163 173 -97 24 -74 86 -102 14 3 -63 21 -5 -118 57 12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDTGTCGGTGRHD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 5273 E= 1.9e-519 0.282572 0.245022 0.130666 0.341741 0.280675 0.128011 0.258297 0.333017 0.293002 0.072255 0.251090 0.383653 0.089892 0.169543 0.229281 0.511284 0.000000 0.000000 1.000000 0.000000 0.164423 0.009672 0.121183 0.704722 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.168405 0.000000 0.831595 0.063152 0.070358 0.722549 0.143941 0.334155 0.130476 0.396359 0.139010 0.311398 0.222075 0.141286 0.325242 0.271572 0.096340 0.324673 0.307415 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDTGTCGGTGRHD MEME-1 regular expression -------------------------------------------------------------------------------- [TAC][TAG][TAG][TG]GTCGGTG[GA][TAC][GTA] -------------------------------------------------------------------------------- Time 72.11 secs. ******************************************************************************** ******************************************************************************** MOTIF WCCDYCTCCDYCTYCDCCKYC MEME-2 width = 21 sites = 1050 llr = 11999 E-value = 1.8e-110 ******************************************************************************** -------------------------------------------------------------------------------- Motif WCCDYCTCCDYCTYCDCCKYC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3::2112:12::2::21:1:: pos.-specific C 168167177:68:69:68158 probability G 2::3::2::3::3::3::41: matrix T 432431532541631532442 bits 2.2 2.0 1.8 1.5 * Relative 1.3 * * * * Entropy 1.1 * * * ** * * (16.5 bits) 0.9 ** * ** ** ** ** * 0.7 ** ** ** ** ** ** ** 0.4 ** ** ** ******** ** 0.2 ******************** 0.0 --------------------- Multilevel TCCTCCTCCTCCTCCTCCTCC consensus ATTGT GT GT GT GT GT sequence A A A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCDYCTCCDYCTYCDCCKYC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 916238 bayes= 12.0475 E= 1.8e-110 -1 -84 -51 65 -296 152 -293 13 -321 180 -1668 -41 -26 -148 20 63 -180 135 -331 28 -132 177 -352 -120 -40 -167 12 77 -1668 174 -784 -6 -223 176 -284 -71 -20 -298 32 69 -1668 142 -308 47 -292 191 -1668 -97 -87 -1668 26 105 -345 156 -1668 23 -321 196 -1668 -124 -19 -1668 40 72 -243 157 -1668 10 -1668 193 -1668 -74 -154 -96 78 56 -282 110 -193 63 -262 182 -1668 -60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCDYCTCCDYCTYCDCCKYC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1050 E= 1.8e-110 0.280952 0.121905 0.153333 0.443810 0.036190 0.625714 0.028571 0.309524 0.030476 0.757143 0.000000 0.212381 0.235238 0.078095 0.250476 0.436190 0.080952 0.555238 0.021905 0.341905 0.113333 0.744762 0.019048 0.122857 0.214286 0.068571 0.236190 0.480952 0.000000 0.727619 0.000952 0.271429 0.060000 0.737143 0.030476 0.172381 0.245714 0.027619 0.271429 0.455238 0.000000 0.582857 0.025714 0.391429 0.037143 0.819048 0.000000 0.143810 0.154286 0.000000 0.260952 0.584762 0.025714 0.642857 0.000000 0.331429 0.030476 0.850476 0.000000 0.119048 0.246667 0.000000 0.288571 0.464762 0.052381 0.645714 0.000000 0.301905 0.000000 0.831429 0.000000 0.168571 0.097143 0.112381 0.374286 0.416190 0.040000 0.466667 0.057143 0.436190 0.045714 0.767619 0.000000 0.186667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCDYCTCCDYCTYCDCCKYC MEME-2 regular expression -------------------------------------------------------------------------------- [TA][CT][CT][TGA][CT]C[TGA][CT]C[TGA][CT]C[TG][CT]C[TGA][CT]C[TG][CT]C -------------------------------------------------------------------------------- Time 137.85 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************