******************************************************************************** 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/AT1G19000_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/AT1G19000_peak_sequences.fasta -dna -oc out/AT1G19000 -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= 3363 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= 514975 N= 3363 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.345 C 0.155 G 0.155 T 0.345 Background letter frequencies (from file dataset with add-one prior applied): A 0.346 C 0.154 G 0.154 T 0.346 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWWTGGATAAGRW MEME-1 width = 13 sites = 3249 llr = 27391 E-value = 1.4e-725 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWWTGGATAAGRW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 45411:a:a9243 pos.-specific C 1::1::::::111 probability G 1:2:9a::::551 matrix T 4548:::a::215 bits 2.7 * 2.4 * 2.2 * 1.9 ** Relative 1.6 **** Entropy 1.3 ***** (12.2 bits) 1.1 ****** 0.8 ****** 0.5 ********* 0.3 * ********* 0.0 ------------- Multilevel AAATGGATAAGGT consensus TTT AAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWTGGATAAGRW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 474619 bayes= 8.80415 E= 1.4e-725 37 -137 -64 19 52 -284 -238 39 26 -163 26 3 -175 -44 -357 116 -148 -1831 251 -1831 -1831 -1831 270 -1831 153 -1831 -1831 -1831 -1831 -1831 -1831 153 147 -406 -538 -352 140 -1831 -180 -295 -76 -34 164 -84 7 -81 155 -183 -24 -32 -93 54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWTGGATAAGRW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 3249 E= 1.4e-725 0.446907 0.059711 0.098492 0.394891 0.494614 0.021545 0.029548 0.454294 0.413050 0.049861 0.184057 0.353032 0.102801 0.113573 0.012927 0.770699 0.124346 0.000000 0.875654 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.956910 0.009234 0.003693 0.030163 0.911050 0.000000 0.044321 0.044629 0.204063 0.121884 0.481071 0.192982 0.363804 0.088027 0.450908 0.097261 0.293013 0.123115 0.080640 0.503232 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWTGGATAAGRW MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][AT]TGGATAA[GA][GA][TA] -------------------------------------------------------------------------------- Time 131.11 secs. ******************************************************************************** ******************************************************************************** MOTIF RARARRAAGAARRAGARRRAR MEME-2 width = 21 sites = 207 llr = 2474 E-value = 1.5e-018 ******************************************************************************** -------------------------------------------------------------------------------- Motif RARARRAAGAARRAGARRRAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 564756783964692a35574 pos.-specific C ::1:1::::1::1:::1:1:: probability G 335344227:253:8:44315 matrix T 121:::::::21::::2::21 bits 2.7 2.4 2.2 1.9 Relative 1.6 * * Entropy 1.3 * ** (17.2 bits) 1.1 * * *** * 0.8 ******* ***** * * 0.5 ********** ***** ** * 0.3 ********************* 0.0 --------------------- Multilevel AAGAAAAAGAAGAAGAGAAAG consensus GGAGGGG A TAG A AGG A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARARRAAGAARRAGARRRAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 447715 bayes= 13.1931 E= 1.5e-018 64 -267 101 -146 67 -1434 81 -95 7 -109 166 -216 98 -1434 91 -358 48 -91 150 -1434 72 -1434 148 -1434 106 -1434 65 -316 118 -267 33 -1434 -43 -1434 227 -1434 133 -109 -267 -335 85 -1434 18 -77 36 -199 159 -270 80 -129 111 -1434 138 -299 -219 -299 -77 -1434 237 -1434 148 -499 -1434 -358 -30 -109 150 -70 66 -399 153 -1434 61 -54 111 -335 93 -219 -14 -103 14 -1434 181 -216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARARRAAGAARRAGARRRAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 207 E= 1.5e-018 0.541063 0.024155 0.309179 0.125604 0.550725 0.000000 0.270531 0.178744 0.362319 0.072464 0.487923 0.077295 0.681159 0.000000 0.289855 0.028986 0.483092 0.082126 0.434783 0.000000 0.570048 0.000000 0.429952 0.000000 0.719807 0.000000 0.241546 0.038647 0.782609 0.024155 0.193237 0.000000 0.256039 0.000000 0.743961 0.000000 0.869565 0.072464 0.024155 0.033816 0.623188 0.000000 0.173913 0.202899 0.444444 0.038647 0.463768 0.053140 0.603865 0.062802 0.333333 0.000000 0.903382 0.019324 0.033816 0.043478 0.202899 0.000000 0.797101 0.000000 0.966184 0.004831 0.000000 0.028986 0.280193 0.072464 0.434783 0.212560 0.545894 0.009662 0.444444 0.000000 0.526570 0.106280 0.333333 0.033816 0.657005 0.033816 0.140097 0.169082 0.381643 0.000000 0.541063 0.077295 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARARRAAGAARRAGARRRAR MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG][GA][AG][AG][AG][AG]A[GA]A[AT][GA][AG]A[GA]A[GAT][AG][AG]A[GA] -------------------------------------------------------------------------------- Time 242.01 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************