******************************************************************************** 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/AT5G56110_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/AT5G56110_peak_sequences.fasta -dna -oc out/AT5G56110 -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= 2706 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= 428867 N= 2706 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.346 C 0.154 G 0.154 T 0.346 Background letter frequencies (from file dataset with add-one prior applied): A 0.346 C 0.153 G 0.153 T 0.346 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWARKTAGGTRR MEME-1 width = 12 sites = 2678 llr = 20063 E-value = 3.2e-486 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWARKTAGGTRR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4575::7:::45 pos.-specific C 2::::::::::1 probability G 12144::a7:43 matrix T 33216a3:2a11 bits 2.7 * 2.4 * 2.2 * 1.9 * Relative 1.6 * *** Entropy 1.4 * *** (10.8 bits) 1.1 ** *** 0.8 ** *** 0.5 ******** 0.3 ********** 0.0 ------------ Multilevel AAAATTAGGTGA consensus TTTGG T T AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWARKTAGGTRR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 399101 bayes= 8.7185 E= 3.2e-486 31 13 -11 -41 50 -176 5 -18 92 -468 -19 -76 58 -588 123 -154 -640 -1803 131 83 -1803 -1803 -1803 153 101 -710 -436 -24 -1803 -1803 270 -1803 -686 -478 228 -51 -1803 -1803 -1803 153 19 -190 155 -160 46 -130 113 -147 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWARKTAGGTRR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 2678 E= 3.2e-486 0.429052 0.168409 0.142270 0.260269 0.489918 0.045183 0.159447 0.305452 0.654966 0.005975 0.134802 0.204257 0.518671 0.002614 0.359970 0.118745 0.004108 0.000000 0.380134 0.615758 0.000000 0.000000 0.000000 1.000000 0.698282 0.001120 0.007468 0.293129 0.000000 0.000000 1.000000 0.000000 0.002987 0.005601 0.747946 0.243465 0.000000 0.000000 0.000000 1.000000 0.395444 0.041075 0.449216 0.114264 0.475728 0.062360 0.336445 0.125467 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWARKTAGGTRR MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][AT][AG][TG]T[AT]G[GT]T[GA][AG] -------------------------------------------------------------------------------- Time 79.59 secs. ******************************************************************************** ******************************************************************************** MOTIF WBCCWAACCAAACCAA MEME-2 width = 16 sites = 9 llr = 139 E-value = 8.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif WBCCWAACCAAACCAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 611149a::8aa119a pos.-specific C :37711:aa:::99:: probability G :3::2::::2::::1: matrix T 42222::::::::::: bits 2.7 ** 2.4 ** 2.2 ** ** 1.9 ** ** Relative 1.6 *** **** * Entropy 1.4 *** **** * (22.2 bits) 1.1 ** *********** 0.8 ** *********** 0.5 **** *********** 0.3 **** *********** 0.0 ---------------- Multilevel ACCCAAACCAAACCAA consensus TGTTG G sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WBCCWAACCAAACCAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 388277 bayes= 15.5311 E= 8.4e+002 68 -982 -982 36 -164 112 112 -64 -164 212 -982 -64 -164 212 -982 -64 36 -47 53 -64 136 -47 -982 -982 153 -982 -982 -982 -982 270 -982 -982 -982 270 -982 -982 117 -982 53 -982 153 -982 -982 -982 153 -982 -982 -982 -164 253 -982 -982 -164 253 -982 -982 136 -982 -47 -982 153 -982 -982 -982 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WBCCWAACCAAACCAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 8.4e+002 0.555556 0.000000 0.000000 0.444444 0.111111 0.333333 0.333333 0.222222 0.111111 0.666667 0.000000 0.222222 0.111111 0.666667 0.000000 0.222222 0.444444 0.111111 0.222222 0.222222 0.888889 0.111111 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.777778 0.000000 0.222222 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.111111 0.888889 0.000000 0.000000 0.888889 0.000000 0.111111 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WBCCWAACCAAACCAA MEME-2 regular expression -------------------------------------------------------------------------------- [AT][CGT][CT][CT][AGT]AACC[AG]AACCAA -------------------------------------------------------------------------------- Time 146.07 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************