******************************************************************************** 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/AT3G01220_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/AT3G01220_peak_sequences.fasta -dna -oc out/AT3G01220 -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= 4525 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= 1187954 N= 4525 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.377 C 0.123 G 0.123 T 0.377 Background letter frequencies (from file dataset with add-one prior applied): A 0.378 C 0.122 G 0.122 T 0.378 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YYAATAATTDA MEME-1 width = 11 sites = 4510 llr = 31113 E-value = 2.9e-067 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYAATAATTDA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 22aa:7a::36 pos.-specific C 34:::2:::11 probability G 1:::::::141 matrix T 44::a::a923 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 *** ** (10.0 bits) 1.2 *** ** 0.9 ******* 0.6 ******** 0.3 ********** 0.0 ----------- Multilevel TCAATAATTGA consensus CT C AT sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYAATAATTDA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1142704 bayes= 10.1506 E= 2.9e-067 -89 119 -24 14 -106 176 -1878 10 140 -1878 -1878 -1878 140 -1878 -1878 -1878 -1878 -1878 -1878 140 95 99 -261 -615 140 -1878 -1878 -1878 -1878 -1878 -1878 140 -348 -593 -58 122 -22 -33 158 -83 62 -62 -71 -51 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYAATAATTDA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 4510 E= 2.9e-067 0.203548 0.277827 0.103548 0.415078 0.181153 0.413747 0.000000 0.405100 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.732151 0.242572 0.019956 0.005322 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.033925 0.001996 0.081596 0.882483 0.325055 0.096896 0.365188 0.212860 0.580931 0.079379 0.074723 0.264967 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYAATAATTDA MEME-1 regular expression -------------------------------------------------------------------------------- [TCA][CT]AAT[AC]ATT[GAT][AT] -------------------------------------------------------------------------------- Time 70.20 secs. ******************************************************************************** ******************************************************************************** MOTIF CCATTTTGTGAAATAAATCYTRGAGTTGRGACTTATTTACARTGGCTGCC MEME-2 width = 50 sites = 13 llr = 650 E-value = 2.0e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCATTTTGTGAAATAAATCYTRGAGTTGRGACTTATTTACARTGGCTGCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2:9:::::::aaa1aa9::2:529:::1429:1:a:::9195:1111112 pos.-specific C 89:31::1:1:::::::175:2::1:1::::8:::1:::8::2:16:188 probability G ::::::18:9::::::::1::47191:868:::1::11:1:5298128:: matrix T :1179a91a::::9::1923a:2::991::1299:9991:1:7:128:1: bits 3.0 2.7 * * 2.4 * * * * 2.1 ** * * * * * * *** Relative 1.8 ** * * * * * * * * *** Entropy 1.5 ** * ****** ** * * * *** * * * ** *** (72.1 bits) 1.2 ** ********* ** ** * ******** * ***** * * ** *** 0.9 ****************************************** *** *** 0.6 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel CCATTTTGTGAAATAAATCCTAGAGTTGGGACTTATTTACAATGGCTGCC consensus C TT G AA T G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATTTTGTGAAATAAATCYTRGAGTTGRGACTTATTTACARTGGCTGCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 966229 bayes= 15.9371 E= 2.0e-020 -129 279 -1035 -1035 -1035 292 -1035 -229 129 -1035 -1035 -229 -1035 133 -1035 87 -1035 -67 -1035 129 -1035 -1035 -1035 140 -1035 -1035 -67 129 -1035 -67 279 -229 -1035 -1035 -1035 140 -1035 -67 292 -1035 140 -1035 -1035 -1035 140 -1035 -1035 -1035 140 -1035 -1035 -1035 -229 -1035 -1035 129 140 -1035 -1035 -1035 140 -1035 -1035 -1035 129 -1035 -1035 -229 -1035 -67 -1035 129 -1035 250 -67 -71 -129 214 -1035 -30 -1035 -1035 -1035 140 29 33 165 -1035 -129 -1035 250 -129 129 -1035 -67 -1035 -1035 -67 292 -1035 -1035 -1035 -67 129 -1035 -67 -1035 129 -229 -1035 279 -229 3 -1035 233 -1035 -71 -1035 265 -1035 129 -1035 -1035 -229 -1035 265 -1035 -71 -229 -1035 -1035 129 -1035 -1035 -67 129 140 -1035 -1035 -1035 -1035 -67 -1035 129 -1035 -1035 -67 129 -1035 -1035 -67 129 129 -1035 -1035 -229 -229 279 -67 -1035 129 -1035 -1035 -229 51 -1035 192 -1035 -1035 33 33 87 -229 -1035 292 -1035 -229 -67 265 -229 -229 233 -67 -71 -229 -1035 33 102 -229 -67 279 -1035 -229 279 -1035 -229 -129 279 -1035 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATTTTGTGAAATAAATCYTRGAGTTGRGACTTATTTACARTGGCTGCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 13 E= 2.0e-020 0.153846 0.846154 0.000000 0.000000 0.000000 0.923077 0.000000 0.076923 0.923077 0.000000 0.000000 0.076923 0.000000 0.307692 0.000000 0.692308 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.076923 0.923077 0.000000 0.076923 0.846154 0.076923 0.000000 0.000000 0.000000 1.000000 0.000000 0.076923 0.923077 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.076923 0.000000 0.000000 0.923077 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.923077 0.000000 0.000000 0.076923 0.000000 0.076923 0.000000 0.923077 0.000000 0.692308 0.076923 0.230769 0.153846 0.538462 0.000000 0.307692 0.000000 0.000000 0.000000 1.000000 0.461538 0.153846 0.384615 0.000000 0.153846 0.000000 0.692308 0.153846 0.923077 0.000000 0.076923 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 0.000000 0.076923 0.923077 0.000000 0.076923 0.000000 0.923077 0.076923 0.000000 0.846154 0.076923 0.384615 0.000000 0.615385 0.000000 0.230769 0.000000 0.769231 0.000000 0.923077 0.000000 0.000000 0.076923 0.000000 0.769231 0.000000 0.230769 0.076923 0.000000 0.000000 0.923077 0.000000 0.000000 0.076923 0.923077 1.000000 0.000000 0.000000 0.000000 0.000000 0.076923 0.000000 0.923077 0.000000 0.000000 0.076923 0.923077 0.000000 0.000000 0.076923 0.923077 0.923077 0.000000 0.000000 0.076923 0.076923 0.846154 0.076923 0.000000 0.923077 0.000000 0.000000 0.076923 0.538462 0.000000 0.461538 0.000000 0.000000 0.153846 0.153846 0.692308 0.076923 0.000000 0.923077 0.000000 0.076923 0.076923 0.769231 0.076923 0.076923 0.615385 0.076923 0.230769 0.076923 0.000000 0.153846 0.769231 0.076923 0.076923 0.846154 0.000000 0.076923 0.846154 0.000000 0.076923 0.153846 0.846154 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCATTTTGTGAAATAAATCYTRGAGTTGRGACTTATTTACARTGGCTGCC MEME-2 regular expression -------------------------------------------------------------------------------- CCA[TC]TTTGTGAAATAAAT[CT][CT]T[AG]GAGTTG[GA][GA]A[CT]TTATTTACA[AG]TGG[CT]TGCC -------------------------------------------------------------------------------- Time 132.80 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************