******************************************************************************** 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/AT1G69570_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/AT1G69570_peak_sequences.fasta -dna -oc out/AT1G69570 -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= 5330 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= 1055171 N= 5330 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.355 C 0.145 G 0.145 T 0.355 Background letter frequencies (from file dataset with add-one prior applied): A 0.356 C 0.144 G 0.144 T 0.356 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAAAARAAAAARWRAAAAAR MEME-1 width = 21 sites = 4520 llr = 39421 E-value = 9.9e-410 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAARAAAAARWRAAAAAR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 577887566a99455888764 pos.-specific C 111:::111::::111:::11 probability G 222113422:11514:11224 matrix T 1:111:111:::13:11:111 bits 2.8 2.5 2.2 2.0 Relative 1.7 Entropy 1.4 * (12.6 bits) 1.1 ** 0.8 * **** ** 0.6 ***** **** ***** 0.3 ************* ******* 0.0 --------------------- Multilevel AAAAAAAAAAAAGAAAAAAAG consensus GG G ATG GGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAARAAAAARWRAAAAAR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 948571 bayes= 9.73893 E= 9.9e-410 63 -11 36 -143 95 -39 16 -307 100 -102 8 -246 115 -224 -42 -237 115 -239 -26 -256 97 -253 82 -404 37 -118 134 -165 77 -27 29 -187 77 -80 67 -212 146 -1879 -535 -428 133 -205 -109 -1879 126 -414 -27 -440 8 -239 190 -259 55 -51 -65 -32 43 -136 155 -307 116 -21 -439 -225 116 -365 -3 -283 121 -204 -50 -306 90 -164 65 -252 67 -107 78 -159 9 -14 142 -174 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAARAAAAARWRAAAAAR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4520 E= 9.9e-410 0.549779 0.133407 0.184292 0.132522 0.686283 0.109956 0.161283 0.042478 0.711726 0.071239 0.152212 0.064823 0.792699 0.030531 0.107743 0.069027 0.792035 0.027434 0.120354 0.060177 0.698894 0.025000 0.254425 0.021681 0.458628 0.063717 0.364381 0.113274 0.607743 0.119027 0.175664 0.097566 0.606858 0.082965 0.228540 0.081637 0.978097 0.000000 0.003540 0.018363 0.897566 0.034735 0.067699 0.000000 0.855310 0.008186 0.119690 0.016814 0.376770 0.027434 0.536726 0.059071 0.522566 0.101327 0.091593 0.284513 0.480973 0.056195 0.420575 0.042257 0.793805 0.124558 0.006858 0.074779 0.797566 0.011504 0.140929 0.050000 0.820796 0.034956 0.101549 0.042699 0.665929 0.046239 0.225664 0.062168 0.565708 0.068363 0.247788 0.118142 0.378319 0.130973 0.384292 0.106416 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAARAAAAARWRAAAAAR MEME-1 regular expression -------------------------------------------------------------------------------- AAAAA[AG][AG]A[AG]AAA[GA][AT][AG]AAA[AG][AG][GA] -------------------------------------------------------------------------------- Time 119.61 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTYACTTTTT MEME-2 width = 11 sites = 5277 llr = 32967 E-value = 4.6e-078 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTYACTTTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 32225::::11 pos.-specific C 11142a::::1 probability G 11211:::::1 matrix T 56632:aaa96 bits 2.8 2.5 * 2.2 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.0 bits) 1.1 **** 0.8 ***** 0.6 ***** 0.3 *** ****** 0.0 ----------- Multilevel TTTCACTTTTT consensus A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYACTTTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1001871 bayes= 9.42576 E= 4.6e-078 -50 -66 -25 59 -93 -116 -15 80 -86 -111 26 67 -105 154 -65 -16 53 32 -15 -101 -697 274 -598 -345 -1901 -471 -548 148 -1901 -957 -657 149 -787 -493 -525 148 -202 -369 -393 132 -167 -8 -42 86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYACTTTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5277 E= 4.6e-078 0.252227 0.090961 0.121471 0.535342 0.186470 0.064431 0.129998 0.619102 0.196134 0.066705 0.172257 0.564904 0.171878 0.418799 0.091719 0.317605 0.513928 0.179269 0.130188 0.176616 0.002843 0.962289 0.002274 0.032594 0.000000 0.005496 0.003222 0.991283 0.000000 0.000190 0.001516 0.998294 0.001516 0.004738 0.003790 0.989956 0.087550 0.011181 0.009475 0.891795 0.112185 0.135873 0.107447 0.644495 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTYACTTTTT MEME-2 regular expression -------------------------------------------------------------------------------- [TA]TT[CT]ACTTTTT -------------------------------------------------------------------------------- Time 226.93 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************