******************************************************************************** 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/AT3G01530_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/AT3G01530_peak_sequences.fasta -dna -oc out/AT3G01530 -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= 6249 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= 1321012 N= 6249 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.334 C 0.166 G 0.166 T 0.334 Background letter frequencies (from file dataset with add-one prior applied): A 0.335 C 0.165 G 0.165 T 0.335 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YHTACCTAAYT MEME-1 width = 11 sites = 6225 llr = 49138 E-value = 4.9e-390 ******************************************************************************** -------------------------------------------------------------------------------- Motif YHTACCTAAYT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2228::3aa12 pos.-specific C 332:aa:::63 probability G 1122::1:::: matrix T 445:::7::35 bits 2.6 ** 2.3 ** 2.1 ** 1.8 ** Relative 1.6 ** * Entropy 1.3 ** ** (11.4 bits) 1.0 *** *** 0.8 *** *** 0.5 ******* 0.3 * ********* 0.0 ----------- Multilevel TTTACCTAACT consensus CC G A TC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHTACCTAAYT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1258522 bayes= 9.59735 E= 4.9e-390 -83 80 -75 34 -53 64 -30 17 -115 -2 -9 67 122 -1925 40 -1002 -686 260 -1925 -1925 -1102 260 -1925 -1102 -38 -1925 -151 103 157 -1925 -525 -1925 151 -191 -1925 -1925 -253 191 -1925 -7 -88 70 -417 69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHTACCTAAYT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6225 E= 4.9e-390 0.188755 0.288193 0.098153 0.424900 0.231325 0.256867 0.133815 0.377992 0.151165 0.162249 0.154699 0.531888 0.781365 0.000000 0.218313 0.000321 0.002892 0.997108 0.000000 0.000000 0.000161 0.999679 0.000000 0.000161 0.257671 0.000000 0.057992 0.684337 0.995663 0.000000 0.004337 0.000000 0.955984 0.044016 0.000000 0.000000 0.058153 0.622008 0.000000 0.319839 0.182329 0.267309 0.009157 0.541205 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHTACCTAAYT MEME-1 regular expression -------------------------------------------------------------------------------- [TC][TCA]T[AG]CC[TA]AA[CT][TC] -------------------------------------------------------------------------------- Time 73.10 secs. ******************************************************************************** ******************************************************************************** MOTIF WAACYRAACCRAACCRAAHH MEME-2 width = 20 sites = 398 llr = 5428 E-value = 1.3e-031 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAACYRAACCRAACCRAAHH MEME-2 Description -------------------------------------------------------------------------------- Simplified A 58511598::4a9:158943 pos.-specific C 1:275::189::1881::34 probability G 1:1:15::::5::::411:: matrix T 31123::121:::21::133 bits 2.6 2.3 2.1 * 1.8 ** Relative 1.6 ** * ** Entropy 1.3 * * ** * ** (19.7 bits) 1.0 * * ** **** ** 0.8 * * ************* 0.5 * *************** * 0.3 ******************* 0.0 -------------------- Multilevel AAACCAAACCGAACCAAAAC consensus T CTTG A G CA sequence TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAACYRAACCRAACCRAAHH MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1202281 bayes= 13.771 E= 1.3e-031 66 -95 -42 -34 133 -1528 -234 -144 69 55 -104 -128 -201 210 -1528 -67 -247 168 -23 -32 61 -213 145 -1528 149 -258 -234 -1528 128 -83 -272 -225 -1528 235 -1528 -106 -606 246 -1528 -193 33 -223 166 -389 158 -1528 -1528 -1528 138 -61 -304 -1528 -1528 230 -287 -104 -170 228 -1528 -185 50 -172 141 -315 131 -1528 -20 -374 136 -1528 -145 -210 33 93 -603 -36 -10 136 -1528 -34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAACYRAACCRAACCRAAHH MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 398 E= 1.3e-031 0.527638 0.085427 0.123116 0.263819 0.844221 0.000000 0.032663 0.123116 0.540201 0.241206 0.080402 0.138191 0.082915 0.706030 0.000000 0.211055 0.060302 0.530151 0.140704 0.268844 0.510050 0.037688 0.452261 0.000000 0.939698 0.027638 0.032663 0.000000 0.811558 0.092965 0.025126 0.070352 0.000000 0.839196 0.000000 0.160804 0.005025 0.907035 0.000000 0.087940 0.422111 0.035176 0.520101 0.022613 1.000000 0.000000 0.000000 0.000000 0.871859 0.108040 0.020101 0.000000 0.000000 0.814070 0.022613 0.163317 0.103015 0.804020 0.000000 0.092965 0.472362 0.050251 0.439698 0.037688 0.831658 0.000000 0.143216 0.025126 0.861809 0.000000 0.060302 0.077889 0.422111 0.314070 0.002513 0.261307 0.311558 0.424623 0.000000 0.263819 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAACYRAACCRAACCRAAHH MEME-2 regular expression -------------------------------------------------------------------------------- [AT]A[AC][CT][CT][AG]AACC[GA]AACC[AG]AA[ACT][CAT] -------------------------------------------------------------------------------- Time 140.39 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************