******************************************************************************** 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/AT4G16750_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/AT4G16750_peak_sequences.fasta -dna -oc out/AT4G16750 -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= 5939 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= 1266595 N= 5939 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.287 C 0.213 G 0.213 T 0.287 Background letter frequencies (from file dataset with add-one prior applied): A 0.29 C 0.21 G 0.21 T 0.29 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HNHCRCCGACAHHD MEME-1 width = 14 sites = 5935 llr = 50289 E-value = 5.5e-491 ******************************************************************************** -------------------------------------------------------------------------------- Motif HNHCRCCGACAHHD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33226:::9:6444 pos.-specific C 3235:aa:1a:221 probability G 13114::a::3113 matrix T 3332::::1:1233 bits 2.2 *** * 2.0 *** * 1.8 *** * 1.6 *** * Relative 1.3 *** * Entropy 1.1 ***** (12.2 bits) 0.9 ****** 0.7 ******* 0.4 ******** 0.2 ********* 0.0 -------------- Multilevel CTTCACCGACAAAA consensus AAC G GCTT sequence TG TCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HNHCRCCGACAHHD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 1189388 bayes= 9.57572 E= 5.5e-491 -4 59 -70 -9 -4 -39 30 4 -65 69 -73 27 -61 134 -112 -69 114 -1918 77 -629 -1918 225 -1918 -705 -1918 225 -1918 -1918 -584 -796 224 -1918 158 -159 -524 -236 -622 224 -796 -794 106 -320 52 -204 41 23 -59 -33 35 6 -61 -7 30 -87 29 -9 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HNHCRCCGACAHHD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 5935 E= 5.5e-491 0.281719 0.316596 0.129065 0.272620 0.282393 0.160573 0.259141 0.297894 0.183993 0.339511 0.126874 0.349621 0.189722 0.533277 0.097051 0.179949 0.637911 0.000000 0.358382 0.003707 0.000000 0.997810 0.000000 0.002190 0.000000 1.000000 0.000000 0.000000 0.005055 0.000842 0.994103 0.000000 0.867902 0.069924 0.005560 0.056613 0.003875 0.994103 0.000842 0.001179 0.605729 0.022915 0.301095 0.070261 0.384330 0.245998 0.139680 0.229992 0.368660 0.218534 0.137658 0.275147 0.357035 0.114743 0.256613 0.271609 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HNHCRCCGACAHHD MEME-1 regular expression -------------------------------------------------------------------------------- [CAT][TAG][TC]C[AG]CCGAC[AG][ACT][ATC][ATG] -------------------------------------------------------------------------------- Time 79.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CGRMGGMGRAGRHGRHGRHGR MEME-2 width = 21 sites = 1389 llr = 15147 E-value = 1.6e-080 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGRMGGMGRAGRHGRHGRHGR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2243135:4624514323413 pos.-specific C 5:15::3::2::2:141:3:1 probability G 175:96:a5175:85176:74 matrix T 2:12::2::1::31:2:1311 bits 2.2 * 2.0 * 1.8 * 1.6 * * Relative 1.3 * * Entropy 1.1 * * * * * (15.7 bits) 0.9 * ** ** * * * * 0.7 * ** ** ** * ** * 0.4 ************** **** 0.2 ********************* 0.0 --------------------- Multilevel CGGCGGAGGAGGAGGCGGAGG consensus AA AC ACAAT AA AT A sequence T C T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGRMGGMGRAGRHGRHGRHGR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1147815 bayes= 12.0039 E= 1.6e-080 -61 122 -56 -71 -61 -224 179 -287 30 -137 128 -244 18 114 -819 -48 -181 -461 205 -295 0 -224 161 -352 80 69 -1708 -90 -1708 -1708 224 -584 61 -280 132 -765 101 15 -152 -140 -45 -273 183 -548 54 -233 123 -275 72 19 -1708 -3 -110 -1708 184 -138 51 -150 114 -256 8 88 -102 -50 -62 -164 182 -607 18 -1708 142 -143 47 42 -1708 13 -133 -367 179 -105 6 -58 106 -127 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGRMGGMGRAGRHGRHGRHGR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1389 E= 1.6e-080 0.190065 0.490281 0.142549 0.177106 0.189345 0.044636 0.726422 0.039597 0.356371 0.081353 0.508999 0.053276 0.327574 0.464363 0.000720 0.207343 0.082793 0.008639 0.871130 0.037437 0.289417 0.044636 0.640749 0.025198 0.504680 0.339813 0.000000 0.155508 0.000000 0.000000 0.994960 0.005040 0.443485 0.030238 0.524838 0.001440 0.583153 0.233981 0.073434 0.109431 0.212383 0.031677 0.749460 0.006479 0.421886 0.041757 0.493161 0.043197 0.475882 0.239741 0.000000 0.284377 0.135349 0.000000 0.753060 0.111591 0.413247 0.074154 0.463643 0.048956 0.305256 0.385889 0.103672 0.205184 0.187905 0.067675 0.740101 0.004320 0.328294 0.000000 0.564435 0.107271 0.401728 0.281497 0.000000 0.316775 0.115191 0.016559 0.728582 0.139669 0.301656 0.141109 0.437005 0.120230 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGRMGGMGRAGRHGRHGRHGR MEME-2 regular expression -------------------------------------------------------------------------------- CG[GA][CAT]G[GA][AC]G[GA][AC][GA][GA][ATC]G[GA][CAT]G[GA][ATC]G[GA] -------------------------------------------------------------------------------- Time 150.23 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************