******************************************************************************** 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/AT1G64620_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/AT1G64620_peak_sequences.fasta -dna -oc out/AT1G64620 -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= 8714 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= 2482584 N= 8714 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 RAAAAARAAAAARAAAAARAA MEME-1 width = 21 sites = 7162 llr = 61848 E-value = 2.1e-206 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAAAARAAAAARAAAAARAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 598878668988456787565 pos.-specific C 211:11:11:::11:1:11:1 probability G 3:1122421121412121322 matrix T ::::1:111::11221:1122 bits 2.9 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 (12.5 bits) 1.1 ** 0.9 *** * ** * 0.6 ******* ***** ** 0.3 ********************* 0.0 --------------------- Multilevel AAAAAAAAAAAAGAAAAAAAA consensus G G G A G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAARAAAAARAAAAARAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2308304 bayes= 10.5536 E= 2.1e-206 41 61 109 -443 124 -15 -311 -776 120 -80 -66 -1945 123 -236 -15 -1134 84 -52 50 -263 113 -143 15 -634 65 -1945 135 -216 80 -87 33 -156 110 -132 -21 -285 125 -695 2 -1134 111 -1945 65 -1945 114 -250 -102 -174 25 -83 166 -272 60 5 9 -115 74 -193 25 -88 101 -121 -4 -226 113 -478 52 -676 92 -38 -91 -142 44 -77 124 -183 67 -152 44 -94 53 -21 51 -117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAARAAAAARAAAAARAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7162 E= 2.1e-206 0.480034 0.209578 0.293633 0.016755 0.858419 0.123988 0.015917 0.001676 0.833706 0.078889 0.087406 0.000000 0.849344 0.026808 0.123708 0.000140 0.650517 0.095783 0.195197 0.058503 0.792097 0.050963 0.152471 0.004468 0.568417 0.000000 0.350321 0.081262 0.628735 0.075398 0.173276 0.122591 0.776040 0.055152 0.118682 0.050126 0.859536 0.001117 0.139207 0.000140 0.783580 0.000000 0.216420 0.000000 0.799637 0.024295 0.067719 0.108350 0.432281 0.077492 0.435353 0.054873 0.547473 0.142837 0.146328 0.163362 0.603183 0.036163 0.164060 0.196593 0.731500 0.059341 0.133762 0.075398 0.793493 0.005027 0.198129 0.003351 0.685423 0.105697 0.073164 0.135716 0.490785 0.080983 0.326306 0.101927 0.576096 0.047892 0.186540 0.189472 0.524155 0.119101 0.195476 0.161268 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAARAAAAARAAAAARAA MEME-1 regular expression -------------------------------------------------------------------------------- [AGC]AAAAA[AG]AAA[AG]A[GA]AAAAA[AG]AA -------------------------------------------------------------------------------- Time 121.82 secs. ******************************************************************************** ******************************************************************************** MOTIF NAAAAAGK MEME-2 width = 8 sites = 8059 llr = 56701 E-value = 1.2e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif NAAAAAGK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 39aaaa:1 pos.-specific C 31:::::1 probability G 3:::::a3 matrix T 2::::::5 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 ***** (10.2 bits) 1.1 ****** 0.9 ****** 0.6 ****** 0.3 ******** 0.0 -------- Multilevel AAAAAAGT consensus C G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 2421586 bayes= 10.4632 E= 1.2e-036 -36 95 90 -89 130 -113 -168 -1962 146 -1962 -1962 -1962 146 -1962 -1962 -1962 146 -1962 -1962 -1962 144 -1962 -281 -1962 -1962 -1962 286 -1962 -186 -21 106 45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 8059 E= 1.2e-036 0.282045 0.266038 0.256732 0.195186 0.894032 0.063035 0.042933 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.980395 0.000000 0.019605 0.000000 0.000000 0.000000 1.000000 0.000000 0.100012 0.119246 0.286264 0.494478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGK MEME-2 regular expression -------------------------------------------------------------------------------- [ACG]AAAAAG[TG] -------------------------------------------------------------------------------- Time 234.43 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************