******************************************************************************** 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/AT3G60490_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/AT3G60490_peak_sequences.fasta -dna -oc out/AT3G60490 -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= 2748 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= 587726 N= 2748 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.285 C 0.215 G 0.215 T 0.285 Background letter frequencies (from file dataset with add-one prior applied): A 0.287 C 0.213 G 0.213 T 0.287 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DKTGTCGGTGR MEME-1 width = 11 sites = 2695 llr = 24521 E-value = 1.6e-574 ******************************************************************************** -------------------------------------------------------------------------------- Motif DKTGTCGGTGR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 32:::::::24 pos.-specific C 123::a::311 probability G 23:a::aa:64 matrix T 447:9:::711 bits 2.2 * *** 2.0 * *** 1.8 * *** 1.6 * *** Relative 1.3 ***** Entropy 1.1 ****** (13.1 bits) 0.9 ******* 0.7 ******** 0.4 ******** 0.2 ********* 0.0 ----------- Multilevel TTTGTCGGTGG consensus AGC C A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DKTGTCGGTGR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 560246 bayes= 10.0031 E= 1.6e-574 6 -81 -6 38 -57 -49 28 46 -411 26 -470 133 -1804 -1804 223 -1804 -295 -1804 -221 167 -1804 223 -1804 -1804 -1804 -1804 223 -1804 -1804 -1804 223 -1804 -1804 60 -1804 124 -57 -151 153 -127 40 -105 88 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DKTGTCGGTGR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2695 E= 1.6e-574 0.300557 0.120965 0.204082 0.374397 0.193692 0.151391 0.258998 0.395918 0.016698 0.254917 0.008163 0.720223 0.000000 0.000000 1.000000 0.000000 0.037106 0.000000 0.046011 0.916883 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.323191 0.000000 0.676809 0.192950 0.074583 0.613358 0.119109 0.378479 0.102412 0.390353 0.128757 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DKTGTCGGTGR MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][TG][TC]GTCGG[TC]G[GA] -------------------------------------------------------------------------------- Time 64.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGRMGGAGRHGGMGRMGRHG MEME-2 width = 21 sites = 797 llr = 8524 E-value = 4.9e-102 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGRMGGAGRHGGMGRMGRHG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 22:43136253334:432342 pos.-specific C 26::4::2::3:15::4112: probability G 51a6187:84166:a517516 matrix T 12::21:2:131:2:121131 bits 2.2 2.0 * * 1.8 * * 1.6 * * Relative 1.3 * * * * Entropy 1.1 * * * * (15.4 bits) 0.9 ** ** * * * * 0.7 ** ** ** ** ** * * 0.4 **** ***** ***** ** * 0.2 ********** ******** * 0.0 --------------------- Multilevel GCGGCGGAGAAGGCGGCGGAG consensus AA AA ACAGCAAA AA ATA sequence C T T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRMGGAGRHGGMGRMGRHG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 532766 bayes= 11.6918 E= 4.9e-102 -40 2 119 -184 -41 138 -195 -72 -625 -423 221 -1628 39 -236 145 -784 11 93 -106 -64 -102 -1628 191 -228 7 -308 162 -393 97 8 -540 -47 -46 -1628 188 -503 89 -540 93 -228 17 55 -108 -12 -5 -276 147 -146 -8 -90 143 -275 32 113 -1628 -71 -275 -1628 217 -1628 36 -1628 135 -171 10 97 -112 -70 -84 -195 177 -232 -4 -91 128 -167 47 9 -96 -10 -40 -1628 159 -102 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRMGGAGRHGGMGRMGRHG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 797 E= 4.9e-102 0.218319 0.215809 0.485571 0.080301 0.215809 0.554580 0.055207 0.174404 0.003764 0.011292 0.984944 0.000000 0.377666 0.041405 0.579674 0.001255 0.309912 0.404015 0.101631 0.184442 0.141782 0.000000 0.799247 0.058971 0.302384 0.025094 0.653701 0.018821 0.563363 0.224592 0.005019 0.207026 0.209536 0.000000 0.781681 0.008783 0.531995 0.005019 0.404015 0.058971 0.323714 0.311167 0.100376 0.264743 0.277290 0.031368 0.587202 0.104141 0.271016 0.114178 0.572146 0.042660 0.357591 0.466750 0.000000 0.175659 0.042660 0.000000 0.957340 0.000000 0.370138 0.000000 0.542033 0.087829 0.307403 0.417817 0.097867 0.176913 0.160602 0.055207 0.726474 0.057716 0.279799 0.112923 0.516939 0.090339 0.397742 0.225847 0.109159 0.267252 0.218319 0.000000 0.639900 0.141782 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGRMGGAGRHGGMGRMGRHG MEME-2 regular expression -------------------------------------------------------------------------------- [GAC][CA]G[GA][CA]G[GA][ACT][GA][AG][ACT][GA][GA][CA]G[GA][CA]G[GA][ATC][GA] -------------------------------------------------------------------------------- Time 131.89 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************