******************************************************************************** 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/AT2G30340_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/AT2G30340_peak_sequences.fasta -dna -oc out/AT2G30340 -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= 2113 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= 389137 N= 2113 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.264 C 0.236 G 0.236 T 0.264 Background letter frequencies (from file dataset with add-one prior applied): A 0.265 C 0.235 G 0.235 T 0.265 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YCKCCGYMDHHTYC MEME-1 width = 14 sites = 2048 llr = 14784 E-value = 2.0e-367 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCKCCGYMDHHTYC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 112::11343222: pos.-specific C 57:aa:44:34159 probability G 1:4::82131:21: matrix T 424::13234453: bits 2.1 ** 1.9 ** 1.7 ** * 1.5 ** * Relative 1.3 *** * Entropy 1.0 * *** * (10.4 bits) 0.8 * *** * 0.6 * *** * 0.4 ****** * ** 0.2 ************** 0.0 -------------- Multilevel CCGCCGCCATTTCC consensus T T TATACGT sequence GCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCKCCGYMDHHTYC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 361668 bayes= 9.76221 E= 2.0e-367 -194 95 -121 51 -200 166 -1764 -48 -64 -1764 85 62 -1764 209 -732 -908 -1764 209 -1764 -1764 -180 -890 178 -120 -125 91 -55 11 21 83 -149 -46 54 -245 9 27 14 25 -177 43 -12 64 -359 48 -48 -136 -3 88 -73 113 -191 -1 -266 197 -890 -280 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCKCCGYMDHHTYC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 2048 E= 2.0e-367 0.069336 0.451660 0.101074 0.377930 0.066406 0.742676 0.000000 0.190918 0.169922 0.000000 0.422363 0.407715 0.000000 0.998047 0.001465 0.000488 0.000000 1.000000 0.000000 0.000000 0.076172 0.000488 0.807617 0.115723 0.111328 0.441895 0.160645 0.286133 0.306152 0.417480 0.083496 0.192871 0.386719 0.042969 0.250488 0.319824 0.293457 0.279297 0.068848 0.358398 0.243652 0.366699 0.019531 0.370117 0.190918 0.091309 0.230469 0.487305 0.160156 0.514160 0.062500 0.263184 0.041992 0.919434 0.000488 0.038086 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCKCCGYMDHHTYC MEME-1 regular expression -------------------------------------------------------------------------------- [CT]C[GT]CCG[CT][CA][ATG][TAC][TCA][TG][CT]C -------------------------------------------------------------------------------- Time 121.24 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTCCCGCCAAAAMCGTAAAHYCRTRWTT MEME-2 width = 29 sites = 51 llr = 1458 E-value = 8.8e-083 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTCCCGCCAAAAMCGTAAAHYCRTRWTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::::aa9a6111aa84:26155:: pos.-specific C :::99a:8a::::39:1:::457:2:::: probability G ::::::a::::::::9:::::::4:5::: matrix T 9aa11::2:::::1::7::2251:7:5aa bits 2.1 1.9 ** ** *** * 1.7 ****** *** * * ** ** 1.5 ******* ***** ** ** ** Relative 1.3 ************* ** *** ** Entropy 1.0 ************* ** *** * ** (41.3 bits) 0.8 ******************** **** ** 0.6 ******************** ******** 0.4 ***************************** 0.2 ***************************** 0.0 ----------------------------- Multilevel TTTCCCGCCAAAAACGTAAAATCATGTTT consensus C CC GCAA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCCGCCAAAAMCGTAAAHYCRTRWTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 329973 bayes= 14.2788 E= 8.8e-083 -276 -1232 -358 183 -1232 -1232 -1232 191 -1232 -1232 -1232 191 -1232 200 -1232 -217 -1232 200 -1232 -217 -1232 203 -258 -1232 -1232 -358 203 -376 -376 181 -1232 -76 -276 203 -1232 -1232 191 -1232 -1232 -1232 191 -1232 -1232 -1232 183 -358 -1232 -276 188 -1232 -1232 -376 124 42 -1232 -217 -176 194 -358 -1232 -217 -1232 200 -1232 -144 -77 -358 149 186 -258 -1232 -1232 191 -1232 -1232 -1232 163 -1232 -358 -76 63 59 -1232 -17 -276 94 -358 89 -59 159 -1232 -117 115 -1232 74 -376 -176 0 -1232 137 89 -1232 112 -1232 83 -358 -358 89 -376 -1232 -1232 188 -1232 -358 -358 186 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCCGCCAAAAMCGTAAAHYCRTRWTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 51 E= 8.8e-083 0.039216 0.000000 0.019608 0.941176 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.941176 0.000000 0.058824 0.000000 0.941176 0.000000 0.058824 0.000000 0.960784 0.039216 0.000000 0.000000 0.019608 0.960784 0.019608 0.019608 0.823529 0.000000 0.156863 0.039216 0.960784 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.941176 0.019608 0.000000 0.039216 0.980392 0.000000 0.000000 0.019608 0.627451 0.313725 0.000000 0.058824 0.078431 0.901961 0.019608 0.000000 0.058824 0.000000 0.941176 0.000000 0.098039 0.137255 0.019608 0.745098 0.960784 0.039216 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.823529 0.000000 0.019608 0.156863 0.411765 0.352941 0.000000 0.235294 0.039216 0.450980 0.019608 0.490196 0.176471 0.705882 0.000000 0.117647 0.588235 0.000000 0.392157 0.019608 0.078431 0.235294 0.000000 0.686275 0.490196 0.000000 0.509804 0.000000 0.470588 0.019608 0.019608 0.490196 0.019608 0.000000 0.000000 0.980392 0.000000 0.019608 0.019608 0.960784 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCCGCCAAAAMCGTAAAHYCRTRWTT MEME-2 regular expression -------------------------------------------------------------------------------- TTTCCCGCCAAAA[AC]CGTAAA[ACT][TC]C[AG][TC][GA][TA]TT -------------------------------------------------------------------------------- Time 228.19 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************