******************************************************************************** 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/AT5G24110_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/AT5G24110_peak_sequences.fasta -dna -oc out/AT5G24110 -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= 2711 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= 566402 N= 2711 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.317 C 0.183 G 0.183 T 0.317 Background letter frequencies (from file dataset with add-one prior applied): A 0.319 C 0.181 G 0.181 T 0.319 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAGTCAACG MEME-1 width = 10 sites = 2710 llr = 25427 E-value = 9.8e-730 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAGTCAACG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 467:::aa:1 pos.-specific C 21:::a::91 probability G 112a:::::6 matrix T 22::a::::2 bits 2.5 * * 2.2 * * 2.0 * * * 1.7 ****** Relative 1.5 ****** Entropy 1.2 ****** (13.5 bits) 1.0 ******* 0.7 ******* 0.5 ******** 0.2 ********* 0.0 ---------- Multilevel AAAGTCAACG consensus T G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTCAACG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 542003 bayes= 9.19812 E= 9.8e-730 49 12 -33 -58 99 -150 -29 -104 122 -377 43 -817 -1805 -594 246 -1805 -643 -1805 -1805 164 -567 246 -1805 -1805 164 -1805 -562 -1805 164 -1805 -794 -658 -349 235 -562 -282 -197 -34 164 -60 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTCAACG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 2710 E= 9.8e-730 0.446494 0.196310 0.144280 0.212915 0.632841 0.064207 0.148339 0.154613 0.742066 0.013284 0.243542 0.001107 0.000000 0.002952 0.997048 0.000000 0.003690 0.000000 0.000000 0.996310 0.006273 0.993727 0.000000 0.000000 0.996310 0.000000 0.003690 0.000000 0.995941 0.000000 0.000738 0.003321 0.028413 0.922878 0.003690 0.045018 0.081550 0.143173 0.564945 0.210332 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAGTCAACG MEME-1 regular expression -------------------------------------------------------------------------------- [AT]A[AG]GTCAAC[GT] -------------------------------------------------------------------------------- Time 68.59 secs. ******************************************************************************** ******************************************************************************** MOTIF GAAGAAGAAGAAGAV MEME-2 width = 15 sites = 320 llr = 3564 E-value = 2.5e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAAGAAGAAGAAGAV MEME-2 Description -------------------------------------------------------------------------------- Simplified A 376196:a6296:93 pos.-specific C :11::1::1::1:13 probability G 732912a:28119:4 matrix T ::1::1::1::3:11 bits 2.5 2.2 * 2.0 * * * 1.7 * * * Relative 1.5 * ** * * Entropy 1.2 ** ** ** * (16.1 bits) 1.0 * ** ** ** ** 0.7 ** ** ** ** ** 0.5 ******** ** ** 0.2 *************** 0.0 --------------- Multilevel GAAGAAGAAGAAGAG consensus AGG G G T C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGAAGAAGAAGAV MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 528448 bayes= 12.7482 E= 2.5e-032 -35 -327 192 -277 110 -169 52 -1497 99 -116 17 -197 -259 -1497 238 -567 148 -1497 -105 -367 89 -77 39 -228 -1497 -1497 242 -350 160 -1497 -1497 -335 83 -33 33 -242 -82 -286 213 -1497 148 -269 -110 -1497 87 -169 -116 -20 -367 -253 237 -509 144 -169 -1497 -203 -21 67 98 -197 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGAAGAAGAAGAV MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 320 E= 2.5e-032 0.250000 0.018750 0.684375 0.046875 0.684375 0.056250 0.259375 0.000000 0.634375 0.081250 0.203125 0.081250 0.053125 0.000000 0.940625 0.006250 0.887500 0.000000 0.087500 0.025000 0.590625 0.106250 0.237500 0.065625 0.000000 0.000000 0.971875 0.028125 0.968750 0.000000 0.000000 0.031250 0.568750 0.143750 0.228125 0.059375 0.181250 0.025000 0.793750 0.000000 0.887500 0.028125 0.084375 0.000000 0.584375 0.056250 0.081250 0.278125 0.025000 0.031250 0.934375 0.009375 0.865625 0.056250 0.000000 0.078125 0.275000 0.287500 0.356250 0.081250 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAAGAAGAAGAAGAV MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG][AG]GA[AG]GA[AG]GA[AT]GA[GCA] -------------------------------------------------------------------------------- Time 130.32 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************