******************************************************************************** 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/AT3G12250_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/AT3G12250_peak_sequences.fasta -dna -oc out/AT3G12250 -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= 3773 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= 714880 N= 3773 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.309 C 0.191 G 0.191 T 0.309 Background letter frequencies (from file dataset with add-one prior applied): A 0.31 C 0.19 G 0.19 T 0.31 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WGATGACGTVRNNDW MEME-1 width = 15 sites = 3769 llr = 31059 E-value = 2.5e-540 ******************************************************************************** -------------------------------------------------------------------------------- Motif WGATGACGTVRNNDW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 326::a:11352333 pos.-specific C 112:::9::4:3311 probability G 152:a::9:332222 matrix T 41:a::1:9123334 bits 2.4 2.2 * 1.9 * * 1.7 ***** Relative 1.4 ***** Entropy 1.2 ***** (11.9 bits) 1.0 ****** 0.7 ****** 0.5 ******** 0.2 ********** 0.0 --------------- Multilevel TGATGACGTCACAAT consensus A G AGTCTA sequence G GTG A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGATGACGTVRNNDW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 662058 bayes= 9.12725 E= 2.5e-540 -12 -36 -36 43 -67 -66 150 -106 91 -14 31 -483 -1852 -1852 -1852 169 -860 -648 233 -288 169 -1852 -1852 -761 -602 218 -1852 -123 -251 -444 230 -1019 -226 -217 -412 151 -9 100 40 -199 71 -255 50 -69 -53 58 23 -15 -5 60 -28 -28 12 -36 34 -18 8 -37 -32 27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGATGACGTVRNNDW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3769 E= 2.5e-540 0.285487 0.148050 0.148050 0.418413 0.194481 0.119926 0.537278 0.148315 0.581321 0.172725 0.235076 0.010878 0.000000 0.000000 0.000000 1.000000 0.000796 0.002123 0.954895 0.042186 0.998408 0.000000 0.000000 0.001592 0.004776 0.862563 0.000000 0.132661 0.054391 0.008756 0.936588 0.000265 0.064739 0.042186 0.010878 0.882197 0.291855 0.379411 0.250730 0.078005 0.507827 0.032369 0.267976 0.191828 0.214911 0.282834 0.222075 0.280180 0.300345 0.288140 0.156540 0.254975 0.338021 0.148050 0.240382 0.273547 0.327673 0.146458 0.152295 0.373574 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGATGACGTVRNNDW MEME-1 regular expression -------------------------------------------------------------------------------- [TA]G[AG]TGACGT[CAG][AG][CTGA][ACT][ATG][TA] -------------------------------------------------------------------------------- Time 70.59 secs. ******************************************************************************** ******************************************************************************** MOTIF RADGRAGARRRAGAARRAGAD MEME-2 width = 21 sites = 664 llr = 7227 E-value = 7.3e-057 ******************************************************************************** -------------------------------------------------------------------------------- Motif RADGRAGARRRAGAARRAGAD MEME-2 Description -------------------------------------------------------------------------------- Simplified A 453267275467185456273 pos.-specific C :12::1::2::2::1:11::1 probability G 62264:82364:922631824 matrix T :131:2::1::1::2::2:12 bits 2.4 2.2 1.9 1.7 * Relative 1.4 * * * Entropy 1.2 * ** * * (15.7 bits) 1.0 * ** ** ** * * 0.7 * ** ** ** ** * ** 0.5 * ***** ***** ** ** 0.2 ** ****************** 0.0 --------------------- Multilevel GAAGAAGAAGAAGAAGAAGAG consensus AGTAGT GGAG AGTAGA sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RADGRAGARRRAGAARRAGAD MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 639420 bayes= 12.1002 E= 7.3e-057 25 -233 164 -1602 82 -117 34 -128 15 -25 21 -16 -53 -212 173 -148 83 -1602 107 -264 109 -100 -233 -59 -93 -1602 210 -360 126 -259 23 -1602 64 -8 41 -188 40 -1602 162 -510 88 -697 117 -1602 111 -7 -193 -164 -136 -1602 221 -1602 138 -1602 1 -1602 82 -83 0 -100 23 -1602 175 -1602 80 -100 84 -360 98 -125 -105 -51 -42 -1602 202 -1602 117 -1602 22 -193 3 -81 91 -50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RADGRAGARRRAGAARRAGAD MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 664 E= 7.3e-057 0.368976 0.037651 0.593373 0.000000 0.548193 0.084337 0.239458 0.128012 0.343373 0.159639 0.219880 0.277108 0.215361 0.043675 0.629518 0.111446 0.551205 0.000000 0.399096 0.049699 0.661145 0.094880 0.037651 0.206325 0.162651 0.000000 0.811747 0.025602 0.745482 0.031627 0.222892 0.000000 0.484940 0.179217 0.251506 0.084337 0.408133 0.000000 0.582831 0.009036 0.570783 0.001506 0.427711 0.000000 0.670181 0.180723 0.049699 0.099398 0.120482 0.000000 0.879518 0.000000 0.808735 0.000000 0.191265 0.000000 0.548193 0.106928 0.189759 0.155120 0.362952 0.000000 0.637048 0.000000 0.540663 0.094880 0.338855 0.025602 0.609940 0.079819 0.091867 0.218373 0.231928 0.000000 0.768072 0.000000 0.697289 0.000000 0.221386 0.081325 0.316265 0.108434 0.355422 0.219880 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RADGRAGARRRAGAARRAGAD MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG][ATG][GA][AG][AT]G[AG][AG][GA][AG]AGAA[GA][AG][AT][GA][AG][GAT] -------------------------------------------------------------------------------- Time 136.02 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************