******************************************************************************** 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/AT3G62420_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/AT3G62420_peak_sequences.fasta -dna -oc out/AT3G62420 -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= 4823 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= 934906 N= 4823 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.306 C 0.194 G 0.194 T 0.306 Background letter frequencies (from file dataset with add-one prior applied): A 0.307 C 0.193 G 0.193 T 0.307 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DNHTGMCACGTS MEME-1 width = 12 sites = 4238 llr = 37859 E-value = 1.4e-540 ******************************************************************************** -------------------------------------------------------------------------------- Motif DNHTGMCACGTS MEME-1 Description -------------------------------------------------------------------------------- Simplified A 333214:a:::2 pos.-specific C 1222:6a:a::4 probability G 22217::::9:4 matrix T 33352:::::a: bits 2.4 * * 2.1 * * 1.9 * ** 1.7 ***** Relative 1.4 ***** Entropy 1.2 ****** (12.9 bits) 0.9 ******* 0.7 ******** 0.5 ******** 0.2 ********* 0.0 ------------ Multilevel AAATGCCACGTG consensus TTT TA C sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DNHTGMCACGTS MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 881853 bayes= 10.0107 E= 1.4e-540 17 -45 -6 10 6 -14 2 1 5 14 -35 5 -81 -8 -54 73 -241 -283 184 -46 30 169 -1869 -1869 -1034 237 -1869 -754 170 -1869 -1869 -664 -776 237 -1869 -676 -275 -312 227 -1869 -1869 -687 -1869 170 -82 96 115 -390 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DNHTGMCACGTS MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 4238 E= 1.4e-540 0.344974 0.141104 0.184993 0.328929 0.319490 0.175083 0.196319 0.309108 0.318546 0.212600 0.151723 0.317131 0.174611 0.183105 0.133082 0.509202 0.057574 0.027135 0.692780 0.222511 0.377065 0.622935 0.000000 0.000000 0.000236 0.998112 0.000000 0.001652 0.996933 0.000000 0.000000 0.003067 0.001416 0.995753 0.000000 0.002832 0.045776 0.022180 0.932043 0.000000 0.000000 0.001652 0.000000 0.998348 0.173903 0.375885 0.429684 0.020529 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DNHTGMCACGTS MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][ATC]T[GT][CA]CACGT[GC] -------------------------------------------------------------------------------- Time 72.35 secs. ******************************************************************************** ******************************************************************************** MOTIF ARARRRAGAARAARAARAAGA MEME-2 width = 21 sites = 966 llr = 10069 E-value = 1.1e-041 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARARRRAGAARAARAARAAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 557455739647837747738 pos.-specific C 1::1:111:1:::::1::1:1 probability G 353353:61253162153:7: matrix T 2:11::2::1::11:1::2:1 bits 2.4 2.1 1.9 1.7 Relative 1.4 Entropy 1.2 * * (15.0 bits) 0.9 * * * ** * * * 0.7 ** * ** ***** ***** 0.5 ** ***** *********** 0.2 ********************* 0.0 --------------------- Multilevel AAAAAAAGAAGAAGAAGAAGA consensus GGGGGG A GAG AG AGTA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRRAGAARAARAARAAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 838446 bayes= 12.036 E= 1.1e-041 78 -157 39 -98 71 -233 125 -1656 111 -1656 56 -251 54 -87 72 -126 71 -230 124 -1656 81 -124 84 -317 125 -152 -233 -90 -8 -131 163 -321 148 -1656 -41 -1656 88 -72 11 -151 46 -1656 146 -272 127 -754 41 -1656 135 -237 -110 -180 9 -1656 165 -217 127 -302 15 -389 114 -89 -120 -117 31 -284 150 -266 111 -315 70 -821 121 -119 -1656 -58 -16 -1656 182 -285 134 -61 -454 -182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRRAGAARAARAARAAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 966 E= 1.1e-041 0.526915 0.065217 0.252588 0.155280 0.503106 0.038302 0.458592 0.000000 0.661491 0.000000 0.284679 0.053830 0.447205 0.105590 0.318841 0.128364 0.503106 0.039337 0.457557 0.000000 0.537267 0.081781 0.346791 0.034161 0.729814 0.067288 0.038302 0.164596 0.290890 0.077640 0.598344 0.033126 0.855072 0.000000 0.144928 0.000000 0.566253 0.116977 0.209110 0.107660 0.422360 0.000000 0.531056 0.046584 0.742236 0.001035 0.256729 0.000000 0.784679 0.037267 0.090062 0.087992 0.327122 0.000000 0.604555 0.068323 0.741201 0.023810 0.214286 0.020704 0.674948 0.104555 0.083851 0.136646 0.379917 0.026915 0.544513 0.048654 0.662526 0.021739 0.314700 0.001035 0.709110 0.084886 0.000000 0.206004 0.275362 0.000000 0.682195 0.042443 0.778468 0.126294 0.008282 0.086957 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARARRRAGAARAARAARAAGA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG][AG][AG][AG][AG]A[GA]A[AG][GA][AG]A[GA][AG]A[GA][AG][AT][GA]A -------------------------------------------------------------------------------- Time 142.97 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************