******************************************************************************** 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/AT2G15740_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/AT2G15740_peak_sequences.fasta -dna -oc out/AT2G15740 -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= 5000 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= 1239515 N= 5000 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.276 C 0.224 G 0.224 T 0.276 Background letter frequencies (from file dataset with add-one prior applied): A 0.277 C 0.223 G 0.223 T 0.277 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WTCKTCKTCKTCKTC MEME-1 width = 15 sites = 2445 llr = 23466 E-value = 1.0e-154 ******************************************************************************** -------------------------------------------------------------------------------- Motif WTCKTCKTCKTCKTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 31:1:::::11:11: pos.-specific C 21a:39:29:38127 probability G 11:5::5::4:14:1 matrix T 48:47148:562472 bits 2.2 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * Entropy 1.1 * ** ** * * (13.8 bits) 0.9 * ** ** * * 0.6 ******** ** ** 0.4 *********** ** 0.2 ************** 0.0 --------------- Multilevel TTCGTCGTCTTCGTC consensus A TC TC GC TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTCKTCKTCKTCKTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1169515 bayes= 11.2185 E= 1.0e-154 14 -27 -94 51 -199 -101 -194 146 -1790 214 -429 -594 -149 -1790 103 69 -1790 39 -1790 135 -682 201 -492 -161 -249 -279 107 70 -385 -5 -1790 147 -419 208 -485 -308 -175 -246 92 71 -205 24 -294 121 -1790 180 -203 -75 -145 -74 87 37 -153 -6 -1790 132 -782 172 -127 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTCKTCKTCKTCKTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2445 E= 1.0e-154 0.303885 0.185685 0.116564 0.393865 0.069530 0.110838 0.058078 0.761554 0.000000 0.984049 0.011452 0.004499 0.098569 0.000000 0.455624 0.445808 0.000000 0.292843 0.000000 0.707157 0.002454 0.899387 0.007362 0.090798 0.049080 0.032311 0.469530 0.449080 0.019223 0.216360 0.000000 0.764417 0.015133 0.944376 0.007771 0.032720 0.082209 0.040491 0.423722 0.453579 0.066667 0.264213 0.029039 0.640082 0.000000 0.780368 0.054806 0.164826 0.101022 0.134151 0.407771 0.357055 0.095706 0.213906 0.000000 0.690389 0.001227 0.735787 0.092434 0.170552 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTCKTCKTCKTCKTC MEME-1 regular expression -------------------------------------------------------------------------------- [TA]TC[GT][TC]C[GT][TC]C[TG][TC]C[GT][TC]C -------------------------------------------------------------------------------- Time 123.48 secs. ******************************************************************************** ******************************************************************************** MOTIF NDAWWCGAYKTCGWT MEME-2 width = 15 sites = 4995 llr = 32543 E-value = 7.1e-085 ******************************************************************************** -------------------------------------------------------------------------------- Motif NDAWWCGAYKTCGWT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 23554::51121131 pos.-specific C 3121:a:14:26:12 probability G 2412::a2:511711 matrix T 33236::36552156 bits 2.2 ** 1.9 ** 1.7 ** 1.5 ** Relative 1.3 ** Entropy 1.1 ** (9.4 bits) 0.9 ** * 0.6 *** ** ** 0.4 *** ** ** * 0.2 ************** 0.0 --------------- Multilevel TGAATCGATTTCGTT consensus CTCTA TCGC A sequence AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NDAWWCGAYKTCGWT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1169515 bayes= 9.92261 E= 7.1e-085 -26 19 -31 27 -14 -171 80 8 75 -5 -92 -47 75 -199 -49 21 39 -236 -912 110 -1893 216 -1893 -1893 -943 -1893 216 -1893 97 -204 -57 -12 -223 79 -1893 101 -233 -252 101 72 -86 -11 -75 88 -216 153 -113 -55 -111 -324 167 -100 5 -138 -84 86 -91 -18 -175 109 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NDAWWCGAYKTCGWT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4995 E= 7.1e-085 0.230831 0.254454 0.180581 0.334134 0.250450 0.068468 0.388989 0.292092 0.466266 0.216416 0.117718 0.199600 0.465265 0.056256 0.158759 0.319720 0.361762 0.043644 0.000400 0.594194 0.000000 1.000000 0.000000 0.000000 0.000400 0.000000 0.999600 0.000000 0.540140 0.054454 0.150951 0.254454 0.059059 0.385185 0.000000 0.555756 0.055055 0.038839 0.450851 0.455255 0.152753 0.206406 0.133133 0.507708 0.061862 0.646847 0.102302 0.188989 0.128128 0.023624 0.709910 0.138338 0.285686 0.086086 0.124925 0.503303 0.147347 0.197197 0.066466 0.588989 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NDAWWCGAYKTCGWT MEME-2 regular expression -------------------------------------------------------------------------------- [TCA][GTA][AC][AT][TA]CG[AT][TC][TG][TC]CG[TA]T -------------------------------------------------------------------------------- Time 235.39 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************