******************************************************************************** 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/AT2G28810_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/AT2G28810_peak_sequences.fasta -dna -oc out/AT2G28810 -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= 5998 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= 1410132 N= 5998 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 AAAAAGWAAAAAAAR MEME-1 width = 15 sites = 5651 llr = 42317 E-value = 6.9e-203 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 989893578897755 pos.-specific C :::1:::11:::111 probability G :11116121112133 matrix T ::::::31::::112 bits 2.9 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 (10.8 bits) 1.1 * * * 0.9 ****** * ** 0.6 ****** **** 0.3 ****** ******** 0.0 --------------- Multilevel AAAAAGAAAAAAAAA consensus AT G GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1326160 bayes= 9.95475 E= 6.9e-203 128 -167 -179 -329 123 -367 0 -783 134 -960 -74 -1911 112 -77 -5 -1911 126 -560 -68 -306 -22 -154 222 -1099 56 -151 -27 -26 87 -38 25 -241 115 -121 -3 -841 111 -161 -7 -321 133 -360 -123 -408 104 -240 65 -487 100 -101 -43 -181 57 -96 97 -157 35 -71 109 -116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5651 E= 6.9e-203 0.879844 0.043178 0.039816 0.037162 0.849761 0.010795 0.137852 0.001593 0.917714 0.000177 0.082109 0.000000 0.786763 0.080694 0.132543 0.000000 0.867811 0.002831 0.085826 0.043532 0.310388 0.047248 0.642187 0.000177 0.534065 0.048310 0.114493 0.303132 0.662538 0.105822 0.163334 0.068306 0.805167 0.059459 0.134313 0.001062 0.784640 0.044948 0.131304 0.039108 0.908689 0.011325 0.058574 0.021412 0.746240 0.026013 0.215360 0.012387 0.725712 0.068306 0.102460 0.103522 0.538489 0.070784 0.268802 0.121925 0.461688 0.084056 0.291984 0.162272 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAR MEME-1 regular expression -------------------------------------------------------------------------------- AAAAA[GA][AT]AAAA[AG]A[AG][AG] -------------------------------------------------------------------------------- Time 117.92 secs. ******************************************************************************** ******************************************************************************** MOTIF NAAAAAGTDAA MEME-2 width = 11 sites = 5980 llr = 39649 E-value = 4.6e-088 ******************************************************************************** -------------------------------------------------------------------------------- Motif NAAAAAGTDAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 389aaa:1465 pos.-specific C 31:::::1:11 probability G 21::::a2221 matrix T 2:1::::6322 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.6 bits) 1.1 **** 0.9 ***** 0.6 ****** 0.3 ******** * 0.0 ----------- Multilevel AAAAAAGTAAA consensus C T T sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGTDAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1350152 bayes= 9.79093 E= 4.6e-088 -16 92 67 -87 118 -108 -82 -327 124 -456 -968 -141 146 -1919 -1919 -1108 146 -1919 -1919 -949 143 -1919 -274 -1108 -604 -1919 285 -850 -257 7 50 73 19 -151 71 -21 67 -88 45 -118 52 0 -20 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGTDAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5980 E= 4.6e-088 0.323913 0.259699 0.218562 0.197826 0.819900 0.064883 0.077759 0.037458 0.857860 0.005853 0.000167 0.136120 0.999833 0.000000 0.000000 0.000167 0.999498 0.000000 0.000000 0.000502 0.979264 0.000000 0.020569 0.000167 0.005518 0.000000 0.993478 0.001003 0.061204 0.144147 0.194649 0.600000 0.413880 0.048328 0.225418 0.312375 0.577258 0.074749 0.187625 0.160368 0.520401 0.137625 0.119565 0.222408 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGTDAA MEME-2 regular expression -------------------------------------------------------------------------------- [ACG]AAAAAGT[ATG]A[AT] -------------------------------------------------------------------------------- Time 226.26 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************