******************************************************************************** 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/AT2G37590_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/AT2G37590_peak_sequences.fasta -dna -oc out/AT2G37590 -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= 6193 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= 1505992 N= 6193 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 TYWCTTTTTYTTTTTTTTTTT MEME-1 width = 21 sites = 6182 llr = 46283 E-value = 5.4e-240 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYWCTTTTTYTTTTTTTTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 124::::11221111111112 pos.-specific C 22171:1:1322212212111 probability G 11:1::::1111:1:111121 matrix T 64429a997466777766666 bits 2.9 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 * * (10.8 bits) 1.1 **** 0.9 ***** 0.6 ****** **** 0.3 * ****************** 0.0 --------------------- Multilevel TTACTTTTTTTTTTTTTTTTT consensus CT C C C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYWCTTTTTYTTTTTTTTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1382132 bayes= 9.78396 E= 5.4e-240 -144 21 -99 82 -77 86 -58 30 31 -4 -179 6 -535 240 -34 -122 -881 -99 -418 135 -592 -452 -573 144 -832 -74 -358 132 -188 -152 -592 123 -199 -88 -65 104 -125 125 -19 14 -107 31 -99 70 -163 67 -53 65 -191 45 -515 97 -226 -5 -125 102 -218 22 -231 101 -227 42 -119 91 -156 -2 -45 82 -162 57 -71 71 -130 12 -36 72 -136 -72 16 78 -102 8 -41 66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYWCTTTTTYTTTTTTTTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6182 E= 5.4e-240 0.133452 0.159010 0.069233 0.638305 0.212067 0.249919 0.091880 0.446134 0.447913 0.133614 0.039793 0.378680 0.008897 0.726626 0.108864 0.155613 0.000809 0.069071 0.007603 0.922517 0.005985 0.005985 0.002588 0.985442 0.001132 0.082174 0.011485 0.905209 0.098350 0.048043 0.002265 0.851343 0.091556 0.074895 0.087512 0.746037 0.152216 0.326593 0.120511 0.400679 0.172274 0.170819 0.069395 0.587512 0.117438 0.218214 0.095115 0.569233 0.096732 0.187803 0.003882 0.711582 0.075542 0.133128 0.057910 0.733420 0.079909 0.160466 0.027823 0.731802 0.075057 0.183921 0.060175 0.680848 0.122614 0.135555 0.100776 0.641055 0.118085 0.204465 0.083953 0.593497 0.147687 0.149304 0.107247 0.595762 0.141702 0.083306 0.154157 0.620835 0.178421 0.145746 0.103688 0.572145 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYWCTTTTTYTTTTTTTTTTT MEME-1 regular expression -------------------------------------------------------------------------------- T[TCA][AT]CTTTTT[TC]T[TC]TTTTT[TC]TTT -------------------------------------------------------------------------------- Time 120.33 secs. ******************************************************************************** ******************************************************************************** MOTIF VAAAAAGK MEME-2 width = 8 sites = 6182 llr = 39797 E-value = 3.7e-059 ******************************************************************************** -------------------------------------------------------------------------------- Motif VAAAAAGK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 489aaa:1 pos.-specific C 21:::::1 probability G 21::::a3 matrix T 2:1::::5 bits 2.9 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.3 bits) 1.1 **** 0.9 ****** 0.6 ****** 0.3 ******** 0.0 -------- Multilevel AAAAAAGT consensus G G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VAAAAAGK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1462641 bayes= 9.86573 E= 3.7e-059 4 54 83 -100 119 -125 -63 -370 128 -1924 -398 -173 146 -1924 -1924 -1924 146 -1924 -573 -1924 146 -1924 -1924 -913 -596 -409 284 -796 -238 -21 115 48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VAAAAAGK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6182 E= 3.7e-059 0.373342 0.200582 0.245228 0.180848 0.825299 0.057748 0.088968 0.027984 0.882239 0.000000 0.008735 0.109026 1.000000 0.000000 0.000000 0.000000 0.997412 0.000000 0.002588 0.000000 0.999353 0.000000 0.000000 0.000647 0.005823 0.008088 0.984633 0.001456 0.069880 0.118894 0.305241 0.505985 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VAAAAAGK MEME-2 regular expression -------------------------------------------------------------------------------- [AGC]AAAAAG[TG] -------------------------------------------------------------------------------- Time 227.35 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************