******************************************************************************** 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/AT1G16490_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/AT1G16490_peak_sequences.fasta -dna -oc out/AT1G16490 -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= 3279 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= 620722 N= 3279 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.308 C 0.192 G 0.192 T 0.308 Background letter frequencies (from file dataset with add-one prior applied): A 0.309 C 0.191 G 0.191 T 0.309 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDDKDGKTTGGTGRR MEME-1 width = 15 sites = 3256 llr = 28288 E-value = 3.3e-599 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDDKDGKTTGGTGRR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 333223::3:::344 pos.-specific C 111:1::::::::11 probability G 3335476::a8:743 matrix T 33433:3a7:2a:11 bits 2.4 * 2.2 * 1.9 * 1.7 * *** Relative 1.4 * *** Entropy 1.2 *** *** (12.5 bits) 1.0 *** **** 0.7 ******** 0.5 * ******** 0.2 ************ 0.0 --------------- Multilevel TTTGGGGTTGGTGGA consensus AAATTAT A AAG sequence GGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDKDGKTTGGTGRR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 574816 bayes= 9.67483 E= 3.3e-599 -4 -102 60 2 -13 -69 43 14 -17 -98 49 22 -47 -277 130 -15 -54 -150 110 1 -23 -628 188 -329 -462 -1831 176 14 -1831 -728 -382 167 -9 -266 -696 113 -1831 -1831 239 -1831 -1831 -647 214 -99 -627 -728 -1831 169 -30 -352 186 -287 38 -164 110 -127 41 -78 79 -105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDKDGKTTGGTGRR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3256 E= 3.3e-599 0.301290 0.094287 0.289926 0.314496 0.282862 0.117936 0.257371 0.341830 0.274877 0.096437 0.267813 0.360872 0.223280 0.027948 0.470209 0.278563 0.212531 0.067568 0.407862 0.312039 0.262899 0.002457 0.703010 0.031634 0.012592 0.000000 0.646806 0.340602 0.000000 0.001229 0.013514 0.985258 0.290233 0.030098 0.001536 0.678133 0.000000 0.000000 1.000000 0.000000 0.000000 0.002150 0.842138 0.155713 0.003993 0.001229 0.000000 0.994779 0.250307 0.016585 0.690725 0.042383 0.402641 0.061425 0.407862 0.128071 0.409705 0.111179 0.330160 0.148956 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDKDGKTTGGTGRR MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][TAG][TAG][GTA][GTA][GA][GT]T[TA]GGT[GA][GA][AG] -------------------------------------------------------------------------------- Time 124.82 secs. ******************************************************************************** ******************************************************************************** MOTIF GGWGGWGGWGGWGGDGGWGRK MEME-2 width = 21 sites = 318 llr = 3871 E-value = 2.5e-051 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGWGGWGGWGGWGGDGGWGRK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1132152243:4:22224241 pos.-specific C ::2::1:11::::11::2112 probability G 78189:7617a:872661664 matrix T 114::32141:62:42141:2 bits 2.4 2.2 * 1.9 * 1.7 * * * Relative 1.4 * ** * * Entropy 1.2 * ** * * (17.6 bits) 1.0 ** ** * ** ** 0.7 ** ** * ***** ** ** 0.5 ** ***** ***** ** ** 0.2 ** ***** ***** ** *** 0.0 --------------------- Multilevel GGTGGAGGAGGTGGTGGAGGG consensus A T ATA A GT T AT sequence C AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGGWGGWGGWGGDGGWGRK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 555142 bayes= 12.953 E= 2.5e-051 -203 -202 194 -110 -162 -1496 215 -253 9 8 -167 40 -95 -260 208 -1496 -171 -1496 219 -303 82 -84 -1496 17 -71 -1496 177 -95 -55 -140 162 -126 35 -79 -79 32 -28 -492 185 -262 -1496 -246 234 -1496 39 -592 -1496 94 -1496 -1496 210 -76 -79 -60 186 -662 -45 -97 31 51 -55 -1496 158 -51 -79 -222 175 -116 45 -25 -160 20 -74 -192 171 -116 19 -106 154 -1496 -106 -7 114 -32 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGGWGGWGGWGGDGGWGRK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 318 E= 2.5e-051 0.075472 0.047170 0.732704 0.144654 0.100629 0.000000 0.845912 0.053459 0.330189 0.201258 0.059748 0.408805 0.160377 0.031447 0.808176 0.000000 0.094340 0.000000 0.867925 0.037736 0.544025 0.106918 0.000000 0.349057 0.188679 0.000000 0.650943 0.160377 0.210692 0.072327 0.588050 0.128931 0.393082 0.110063 0.110063 0.386792 0.254717 0.006289 0.688679 0.050314 0.000000 0.034591 0.965409 0.000000 0.405660 0.003145 0.000000 0.591195 0.000000 0.000000 0.817610 0.182390 0.179245 0.125786 0.691824 0.003145 0.226415 0.097484 0.235849 0.440252 0.210692 0.000000 0.572327 0.216981 0.179245 0.040881 0.641509 0.138365 0.421384 0.160377 0.062893 0.355346 0.185535 0.050314 0.625786 0.138365 0.352201 0.091195 0.556604 0.000000 0.147799 0.182390 0.421384 0.248428 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGWGGWGGWGGWGGDGGWGRK MEME-2 regular expression -------------------------------------------------------------------------------- GG[TAC]GG[AT]G[GA][AT][GA]G[TA]GG[TGA][GTA]G[AT]G[GA][GT] -------------------------------------------------------------------------------- Time 232.72 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************