******************************************************************************** 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/AT5G13790_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/AT5G13790_peak_sequences.fasta -dna -oc out/AT5G13790 -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= 1284 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= 181585 N= 1284 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.343 C 0.157 G 0.157 T 0.343 Background letter frequencies (from file dataset with add-one prior applied): A 0.344 C 0.155 G 0.155 T 0.344 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTCCWTTTTDGGWA MEME-1 width = 15 sites = 1222 llr = 11269 E-value = 2.5e-991 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTCCWTTTTDGGWA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:2::3231223:57 pos.-specific C :::a711::11::11 probability G ::1::11:::2791: matrix T 9a7:3567974:132 bits 2.7 * 2.4 * 2.1 * 1.9 * * Relative 1.6 * * Entropy 1.3 * ** ** (13.3 bits) 1.1 * ** * ** 0.8 ** ** * ** 0.5 ***** ** ** * 0.3 ***** **** ** * 0.0 --------------- Multilevel TTTCCTTTTTTGGAA consensus TA A GA T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCWTTTTDGGWA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 163609 bayes= 7.96097 E= 2.5e-991 -224 -190 -457 135 -413 -757 -525 150 -98 -262 -162 112 -639 267 -598 -572 -1690 215 -1690 -14 -5 -36 -91 43 -89 -43 -109 86 -8 -387 -1690 95 -267 -376 -1690 144 -91 -66 -208 98 -54 -116 68 36 -23 -1690 218 -1690 -463 -440 252 -198 49 -38 -76 -18 112 -132 -211 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCWTTTTDGGWA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1222 E= 2.5e-991 0.072831 0.041735 0.006547 0.878887 0.019640 0.000818 0.004092 0.975450 0.174304 0.025368 0.050736 0.749591 0.004092 0.986907 0.002455 0.006547 0.000000 0.688216 0.000000 0.311784 0.333061 0.121113 0.082651 0.463175 0.185761 0.115385 0.072831 0.626023 0.325696 0.010638 0.000000 0.663666 0.054010 0.011457 0.000000 0.934534 0.183306 0.098200 0.036825 0.681669 0.237316 0.069558 0.249591 0.443535 0.293781 0.000000 0.706219 0.000000 0.013912 0.007365 0.891162 0.087561 0.484452 0.119476 0.091653 0.304419 0.747136 0.062193 0.036007 0.154664 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCWTTTTDGGWA MEME-1 regular expression -------------------------------------------------------------------------------- TTTC[CT][TA]T[TA]TT[TGA][GA]G[AT]A -------------------------------------------------------------------------------- Time 83.15 secs. ******************************************************************************** ******************************************************************************** MOTIF TTAATTTATCGATAAATTRAWACYYCTCTAAWTTAATAAAA MEME-2 width = 41 sites = 23 llr = 796 E-value = 2.2e-076 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTAATTTATCGATAAATTRAWACYYCTCTAAWTTAATAAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::aa:::8:11a:7aa::77673:::31:777::a7:a9aa pos.-specific C :::::::226::33:::3::::7638:8:::::::3::::: probability G 3::::::::39:::::::33::::::::332:::::::1:: matrix T 7a::aaa:8:::7:::a7::43:472717::3aa::a:::: bits 2.7 2.4 2.1 * 1.9 * Relative 1.6 *** ** ** *** * * * * Entropy 1.3 ****** ** *** * * *** ***** (50.0 bits) 1.1 ******************** **** * * ********* 0.8 ******************** **** **** ********* 0.5 ***************************************** 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel TTAATTTATCGATAAATTAAAACCTCTCTAAATTAATAAAA consensus G C G CC CGGTTATCTA GGGT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAATTTATCGATAAATTRAWACYYCTCTAAWTTAATAAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 130225 bayes= 11.1878 E= 2.2e-076 -1117 -1117 97 101 -1117 -1117 -1117 154 154 -1117 -1117 -1117 154 -1117 -1117 -1117 -298 -1117 -1117 147 -1117 -1117 -1117 154 -1117 -1117 -1117 154 118 48 -1117 -1117 -1117 16 -1117 126 -198 197 75 -298 -198 -1117 255 -1117 154 -1117 -1117 -1117 -1117 97 -1117 101 101 97 -1117 -1117 154 -1117 -1117 -1117 154 -1117 -1117 -1117 -1117 -1117 -1117 154 -1117 97 -1117 101 92 -1117 116 -1117 101 -1117 97 -1117 71 -1117 -1117 34 101 -1117 -1117 -18 -18 207 -1117 -298 -1117 186 -1117 34 -1117 116 -1117 92 -1117 233 -1117 -66 -18 -1117 -1117 101 -198 233 -1117 -140 -298 -1117 97 92 101 -1117 97 -1117 110 -1117 48 -298 92 -1117 -1117 1 -1117 -1117 -1117 154 -298 -1117 -1117 147 147 -1117 -1117 -298 110 75 -1117 -1117 -298 -1117 -1117 147 154 -1117 -1117 -1117 141 -1117 -84 -1117 154 -1117 -1117 -1117 147 -1117 -1117 -298 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAATTTATCGATAAATTRAWACYYCTCTAAWTTAATAAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 23 E= 2.2e-076 0.000000 0.000000 0.304348 0.695652 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.043478 0.000000 0.000000 0.956522 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.782609 0.217391 0.000000 0.000000 0.000000 0.173913 0.000000 0.826087 0.086957 0.608696 0.260870 0.043478 0.086957 0.000000 0.913043 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.304348 0.000000 0.695652 0.695652 0.304348 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.304348 0.000000 0.695652 0.652174 0.000000 0.347826 0.000000 0.695652 0.000000 0.304348 0.000000 0.565217 0.000000 0.000000 0.434783 0.695652 0.000000 0.000000 0.304348 0.304348 0.652174 0.000000 0.043478 0.000000 0.565217 0.000000 0.434783 0.000000 0.347826 0.000000 0.652174 0.000000 0.782609 0.000000 0.217391 0.304348 0.000000 0.000000 0.695652 0.086957 0.782609 0.000000 0.130435 0.043478 0.000000 0.304348 0.652174 0.695652 0.000000 0.304348 0.000000 0.739130 0.000000 0.217391 0.043478 0.652174 0.000000 0.000000 0.347826 0.000000 0.000000 0.000000 1.000000 0.043478 0.000000 0.000000 0.956522 0.956522 0.000000 0.000000 0.043478 0.739130 0.260870 0.000000 0.000000 0.043478 0.000000 0.000000 0.956522 1.000000 0.000000 0.000000 0.000000 0.913043 0.000000 0.086957 0.000000 1.000000 0.000000 0.000000 0.000000 0.956522 0.000000 0.000000 0.043478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAATTTATCGATAAATTRAWACYYCTCTAAWTTAATAAAA MEME-2 regular expression -------------------------------------------------------------------------------- [TG]TAATTT[AC]T[CG]GA[TC][AC]AAT[TC][AG][AG][AT][AT][CA][CT][TC][CT][TA]C[TG][AG][AG][AT]TTA[AC]TAAAA -------------------------------------------------------------------------------- Time 151.94 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************