******************************************************************************** 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/AT1G79180_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/AT1G79180_peak_sequences.fasta -dna -oc out/AT1G79180 -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= 4203 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= 764099 N= 4203 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 0.308 C 0.192 G 0.192 T 0.308 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDDDKGGTWGGTGRR MEME-1 width = 15 sites = 4150 llr = 36087 E-value = 3.1e-643 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDDDKGGTWGGTGRR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 333223::3:::244 pos.-specific C 111:1:::::::::1 probability G 3235477::a8:743 matrix T 33333:3a6:2a:11 bits 2.4 * 2.1 * 1.9 * 1.7 * *** Relative 1.4 * *** Entropy 1.2 *** **** (12.5 bits) 1.0 *** **** 0.7 *** **** 0.5 * ********* 0.2 ************ 0.0 --------------- Multilevel ATTGGGGTTGGTGAA consensus TAATTAT A AGG sequence GGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDDKGGTWGGTGRR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 705257 bayes= 9.68525 E= 3.1e-643 7 -93 56 -7 -10 -63 37 14 -8 -89 49 12 -39 -293 128 -17 -57 -164 111 4 -12 -764 185 -379 -451 -1866 179 7 -483 -806 -1866 168 5 -257 -300 102 -1866 -1866 238 -1866 -1866 -1866 214 -99 -732 -573 -1866 169 -30 -378 188 -338 53 -205 101 -136 41 -82 79 -104 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDDKGGTWGGTGRR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4150 E= 3.1e-643 0.321928 0.101205 0.283855 0.293012 0.287229 0.124096 0.249157 0.339518 0.290602 0.103855 0.270602 0.334940 0.234940 0.025301 0.467229 0.272530 0.206747 0.061687 0.414699 0.316867 0.283133 0.000964 0.693735 0.022169 0.013494 0.000000 0.663133 0.323373 0.010843 0.000723 0.000000 0.988434 0.318554 0.032289 0.024096 0.625060 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.845542 0.154458 0.001928 0.003614 0.000000 0.994458 0.249157 0.013976 0.707229 0.029639 0.444819 0.046506 0.388675 0.120000 0.409880 0.108916 0.332048 0.149157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDDKGGTWGGTGRR MEME-1 regular expression -------------------------------------------------------------------------------- [ATG][TAG][TAG][GTA][GTA][GA][GT]T[TA]GGT[GA][AG][AG] -------------------------------------------------------------------------------- Time 123.83 secs. ******************************************************************************** ******************************************************************************** MOTIF ARAARRARAARRARA MEME-2 width = 15 sites = 735 llr = 7293 E-value = 1.2e-025 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARAARRARAARRARA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 837766948767a47 pos.-specific C :211::::1:::::1 probability G :53244162243:62 matrix T 1::::1::::::::: bits 2.4 2.1 1.9 1.7 * Relative 1.4 * Entropy 1.2 * ** (14.3 bits) 1.0 * * ******** 0.7 *************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel AGAAAAAGAAAAAGA consensus AG GG A GGG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARRARAARRARA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 705257 bayes= 12.1663 E= 1.2e-025 145 -197 -344 -171 -4 -13 145 -1617 112 -179 46 -450 126 -110 -16 -1617 86 -1617 118 -550 92 -456 90 -257 154 -514 -95 -1617 32 -324 158 -401 133 -165 -24 -1617 122 -210 32 -1617 96 -1617 106 -1617 110 -1617 82 -1617 170 -1617 -1617 -1617 33 -614 166 -1617 127 -106 -21 -1617 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARRARAARRARA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 735 E= 1.2e-025 0.839456 0.048980 0.017687 0.093878 0.299320 0.175510 0.525170 0.000000 0.666667 0.055782 0.263946 0.013605 0.737415 0.089796 0.172789 0.000000 0.556463 0.000000 0.436735 0.006803 0.580952 0.008163 0.359184 0.051701 0.895238 0.005442 0.099320 0.000000 0.383673 0.020408 0.576871 0.019048 0.775510 0.061224 0.163265 0.000000 0.715646 0.044898 0.239456 0.000000 0.600000 0.000000 0.400000 0.000000 0.661224 0.000000 0.338776 0.000000 1.000000 0.000000 0.000000 0.000000 0.387755 0.002721 0.609524 0.000000 0.741497 0.092517 0.165986 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARRARAARRARA MEME-2 regular expression -------------------------------------------------------------------------------- A[GA][AG]A[AG][AG]A[GA]A[AG][AG][AG]A[GA]A -------------------------------------------------------------------------------- Time 233.19 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************