******************************************************************************** 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/AT2G40740_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/AT2G40740_peak_sequences.fasta -dna -oc out/AT2G40740 -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= 6016 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= 1186837 N= 6016 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.316 C 0.184 G 0.184 T 0.316 Background letter frequencies (from file dataset with add-one prior applied): A 0.318 C 0.182 G 0.182 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HWAAGTCAAC MEME-1 width = 10 sites = 5945 llr = 48560 E-value = 4.3e-477 ******************************************************************************** -------------------------------------------------------------------------------- Motif HWAAGTCAAC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3467:::aa2 pos.-specific C 221:::a::7 probability G 1123a::::: matrix T 332::a:::1 bits 2.5 * * 2.2 * * 2.0 * * 1.7 ***** Relative 1.5 ***** Entropy 1.2 ***** (11.8 bits) 1.0 ****** 0.7 ******* 0.5 ******* 0.2 ******** 0.0 ---------- Multilevel AAAAGTCAAC consensus TTTG sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HWAAGTCAAC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1132693 bayes= 9.83339 E= 4.3e-477 8 38 -61 -5 35 10 -57 -21 79 -107 -19 -65 115 -301 56 -698 -1918 -1918 246 -830 -1918 -1918 -1918 165 -730 246 -1918 -1918 165 -1918 -1918 -1918 165 -1918 -1918 -772 -88 187 -206 -143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HWAAGTCAAC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5945 E= 4.3e-477 0.336585 0.237174 0.118755 0.307485 0.406897 0.194954 0.122624 0.275526 0.550715 0.086627 0.159294 0.203364 0.707149 0.022540 0.267788 0.002523 0.000000 0.000000 0.998991 0.001009 0.000000 0.000000 0.000000 1.000000 0.002019 0.997981 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.998486 0.000000 0.000000 0.001514 0.173255 0.664760 0.043566 0.118419 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HWAAGTCAAC MEME-1 regular expression -------------------------------------------------------------------------------- [ATC][AT][AT][AG]GTCAAC -------------------------------------------------------------------------------- Time 121.89 secs. ******************************************************************************** ******************************************************************************** MOTIF ARARRAAGAARAAGARRAAGA MEME-2 width = 21 sites = 1057 llr = 10885 E-value = 1.1e-034 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARARRAAGAARAAGARRAAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 547537738648639547817 pos.-specific C 1::21111:2:12::111111 probability G 163251161251171352:71 matrix T 3::11:::::1:2:11::1:1 bits 2.5 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 * (14.9 bits) 1.0 ** ** * ** * 0.7 ** * ** ** ** **** 0.5 ** ******** ** ***** 0.2 ********************* 0.0 --------------------- Multilevel AGAAGAAGAAGAAGAAGAAGA consensus TAGGA A A A GA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRAAGAARAAGARRAAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1066517 bayes= 12.1354 E= 1.1e-034 73 -103 -48 -34 42 -758 161 -422 120 -1669 49 -481 57 -13 40 -137 6 -77 139 -190 121 -116 -32 -304 116 -40 -82 -269 -12 -159 183 -1669 136 -238 -46 -459 101 -7 -16 -381 36 -1669 157 -261 137 -102 -108 -1669 88 -13 -99 -104 0 -359 187 -1669 143 -400 -142 -229 71 -44 67 -249 23 -150 158 -415 122 -114 -6 -1669 129 -99 -1669 -130 -110 -75 198 -349 122 -118 -114 -172 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRAAGAARAAGARRAAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1057 E= 1.1e-034 0.528855 0.088931 0.130558 0.251656 0.425733 0.000946 0.556291 0.017029 0.733207 0.000000 0.255440 0.011353 0.472091 0.165563 0.239357 0.122990 0.332072 0.106906 0.475875 0.085147 0.734153 0.081362 0.145695 0.038789 0.709555 0.138127 0.103122 0.049196 0.293283 0.060549 0.646168 0.000000 0.819300 0.035005 0.132450 0.013245 0.641438 0.173132 0.162725 0.022706 0.408704 0.000000 0.539262 0.052034 0.824030 0.089877 0.086093 0.000000 0.587512 0.165563 0.091769 0.155156 0.318827 0.015137 0.666036 0.000000 0.855251 0.011353 0.068117 0.065279 0.519395 0.134342 0.289499 0.056764 0.373699 0.064333 0.543992 0.017975 0.743614 0.082308 0.174078 0.000000 0.778619 0.091769 0.000000 0.129612 0.148534 0.107852 0.715232 0.028382 0.740776 0.080416 0.082308 0.096500 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRAAGAARAAGARRAAGA MEME-2 regular expression -------------------------------------------------------------------------------- [AT][GA][AG][AG][GA]AA[GA]AA[GA]AA[GA]A[AG][GA]AAGA -------------------------------------------------------------------------------- Time 230.59 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************