******************************************************************************** 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/AT5G52830_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/AT5G52830_peak_sequences.fasta -dna -oc out/AT5G52830 -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= 3018 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= 615153 N= 3018 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.332 C 0.168 G 0.168 T 0.332 Background letter frequencies (from file dataset with add-one prior applied): A 0.334 C 0.167 G 0.167 T 0.334 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HAAAAGTCAACKNW MEME-1 width = 14 sites = 3016 llr = 27490 E-value = 1.3e-646 ******************************************************************************** -------------------------------------------------------------------------------- Motif HAAAAGTCAACKNW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 45778:::aa2133 pos.-specific C 221::::a::7232 probability G 111:2a:::::421 matrix T 2222::a::::335 bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * Relative 1.6 ***** Entropy 1.3 ****** (13.1 bits) 1.0 ****** 0.8 ******* 0.5 ******** 0.3 *********** 0.0 -------------- Multilevel AAAAAGTCAACGAT consensus T T ATCA sequence C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAAAAGTCAACKNW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 575919 bayes= 9.16606 E= 1.3e-646 25 39 -28 -43 71 -15 -60 -78 98 -129 -108 -77 115 -333 -195 -73 128 -597 -13 -329 -617 -1820 257 -597 -997 -565 -1820 158 -539 257 -797 -1820 157 -616 -565 -665 156 -1820 -361 -589 -57 213 -1820 -290 -132 -14 124 -6 -14 69 5 -37 -39 3 -68 50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAAAAGTCAACKNW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 3016 E= 1.3e-646 0.396220 0.218501 0.137599 0.247679 0.545756 0.150199 0.110080 0.193966 0.658156 0.068302 0.078581 0.194960 0.739058 0.016578 0.043103 0.201260 0.811008 0.002653 0.152188 0.034151 0.004642 0.000000 0.990053 0.005305 0.000332 0.003316 0.000000 0.996353 0.007958 0.991379 0.000663 0.000000 0.991048 0.002321 0.003316 0.003316 0.980769 0.000000 0.013594 0.005637 0.225133 0.730106 0.000000 0.044761 0.133621 0.151525 0.393899 0.320955 0.301724 0.268236 0.172745 0.257294 0.254973 0.170093 0.103780 0.471154 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAAAAGTCAACKNW MEME-1 regular expression -------------------------------------------------------------------------------- [ATC]AA[AT]AGTCAA[CA][GT][ACT][TA] -------------------------------------------------------------------------------- Time 75.02 secs. ******************************************************************************** ******************************************************************************** MOTIF RGAAGAAGAAGAAG MEME-2 width = 14 sites = 281 llr = 3090 E-value = 6.8e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGAAGAAGAAGAAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 42772871a7:98: pos.-specific C 21:1:11::1:::: probability G 27328119:1911a matrix T 2:::::1::1::2: bits 2.6 * 2.3 * 2.1 * * 1.8 * * * Relative 1.6 * ** * * Entropy 1.3 * ** * * (15.9 bits) 1.0 ** * ** ** * 0.8 ***** ** **** 0.5 ***** ******* 0.3 ************* 0.0 -------------- Multilevel AGAAGAAGAAGAAG consensus GAG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAAGAAGAAGAAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 575919 bayes= 13.1673 E= 6.8e-025 31 15 41 -88 -44 -96 201 -1478 112 -1478 74 -1478 114 -130 23 -1478 -60 -1478 223 -1478 132 -146 -109 -355 104 -79 -116 -123 -151 -1478 241 -1478 156 -323 -1478 -1478 116 -96 -59 -255 -423 -185 242 -296 138 -274 -96 -396 118 -1478 -164 -82 -555 -1478 258 -1478 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAAGAAGAAGAAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 281 E= 6.8e-025 0.412811 0.185053 0.220641 0.181495 0.245552 0.085409 0.669039 0.000000 0.722420 0.000000 0.277580 0.000000 0.736655 0.067616 0.195730 0.000000 0.220641 0.000000 0.779359 0.000000 0.832740 0.060498 0.078292 0.028470 0.686833 0.096085 0.074733 0.142349 0.117438 0.000000 0.882562 0.000000 0.982206 0.017794 0.000000 0.000000 0.747331 0.085409 0.110320 0.056940 0.017794 0.046263 0.893238 0.042705 0.868327 0.024911 0.085409 0.021352 0.758007 0.000000 0.053381 0.188612 0.007117 0.000000 0.992883 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAAGAAGAAGAAG MEME-2 regular expression -------------------------------------------------------------------------------- [AG][GA][AG]A[GA]AAGAAGAAG -------------------------------------------------------------------------------- Time 144.54 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************