******************************************************************************** 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/AT1G12610_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/AT1G12610_peak_sequences.fasta -dna -oc out/AT1G12610 -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= 2753 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= 603906 N= 2753 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.301 C 0.199 G 0.199 T 0.301 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NATGTCGGCRR MEME-1 width = 11 sites = 2690 llr = 24313 E-value = 1.4e-527 ******************************************************************************** -------------------------------------------------------------------------------- Motif NATGTCGGCRR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 281::::3:45 pos.-specific C 2:1::a::711 probability G 311a::a7:33 matrix T 317:a:::322 bits 2.3 * ** 2.1 * ** 1.9 * ** 1.6 **** Relative 1.4 **** * Entropy 1.2 ****** (13.0 bits) 0.9 ****** 0.7 * ****** 0.5 ******** 0.2 ********** 0.0 ----------- Multilevel GATGTCGGCAA consensus T ATGG sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NATGTCGGCRR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 576376 bayes= 9.81222 E= 1.4e-527 -44 8 65 -22 137 -274 -100 -179 -169 -70 -181 126 -1804 -1804 235 -1804 -1804 -1804 -1804 172 -1804 235 -1804 -1804 -1804 -1804 235 -1804 3 -1804 182 -1804 -1804 191 -1804 -21 28 -47 78 -100 59 -60 36 -91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NATGTCGGCRR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2690 E= 1.4e-527 0.223420 0.207063 0.308178 0.261338 0.784758 0.029368 0.097770 0.088104 0.094052 0.120446 0.056134 0.729368 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.309294 0.000000 0.690706 0.000000 0.000000 0.736803 0.000000 0.263197 0.369517 0.142007 0.336059 0.152416 0.456877 0.129368 0.251673 0.162082 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NATGTCGGCRR MEME-1 regular expression -------------------------------------------------------------------------------- [GTAC]ATGTCG[GA][CT][AG][AG] -------------------------------------------------------------------------------- Time 119.68 secs. ******************************************************************************** ******************************************************************************** MOTIF ARARRAARARRAARARARARA MEME-2 width = 21 sites = 687 llr = 7134 E-value = 1.1e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARARRAARARRAARARARARA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 658557a48657959466735 pos.-specific C 21111::::11::1:21::11 probability G 241352:61333:5:334152 matrix T 1:11:::::1::1:12::122 bits 2.3 2.1 1.9 1.6 * Relative 1.4 * * Entropy 1.2 ** * * (15.0 bits) 0.9 **** * * 0.7 ** ***** **** ** 0.5 *** *********** **** 0.2 *************** ***** 0.0 --------------------- Multilevel AAAAGAAGAAAAAAAAAAAGA consensus G GAG A GGG G GGG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRAARARRAARARARARA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 548846 bayes= 11.9302 E= 1.1e-050 101 -29 -25 -228 64 -129 117 -612 131 -140 -103 -198 82 -95 54 -198 61 -165 127 -1607 127 -203 14 -1607 168 -1607 -299 -1607 55 -707 150 -1607 147 -203 -101 -470 90 -158 65 -235 85 -124 81 -362 120 -361 41 -354 154 -203 -1607 -209 67 -187 124 -1607 160 -1607 -1607 -190 36 -14 51 -98 103 -172 46 -262 88 -207 100 -1607 129 -217 -112 -130 -27 -152 136 -79 85 -152 -5 -63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRAARARRAARARARARA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 687 E= 1.1e-050 0.612809 0.160116 0.164483 0.062591 0.473071 0.080058 0.442504 0.004367 0.752547 0.074236 0.096070 0.077147 0.535662 0.101892 0.285298 0.077147 0.462882 0.062591 0.474527 0.000000 0.735080 0.048035 0.216885 0.000000 0.975255 0.000000 0.024745 0.000000 0.443959 0.001456 0.554585 0.000000 0.842795 0.048035 0.097525 0.011645 0.567686 0.065502 0.307132 0.059680 0.548763 0.082969 0.343523 0.024745 0.697234 0.016012 0.260553 0.026201 0.880640 0.048035 0.000000 0.071325 0.483261 0.053857 0.462882 0.000000 0.918486 0.000000 0.000000 0.081514 0.388646 0.177584 0.279476 0.154294 0.621543 0.059680 0.269287 0.049491 0.560408 0.046579 0.393013 0.000000 0.742358 0.043668 0.090247 0.123726 0.251820 0.068413 0.503639 0.176128 0.545852 0.068413 0.189229 0.196507 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRAARARRAARARARARA MEME-2 regular expression -------------------------------------------------------------------------------- A[AG]A[AG][GA][AG]A[GA]A[AG][AG][AG]A[AG]A[AG][AG][AG]A[GA]A -------------------------------------------------------------------------------- Time 229.66 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************