******************************************************************************** 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/AT1G72740_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/AT1G72740_peak_sequences.fasta -dna -oc out/AT1G72740 -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= 2886 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= 582672 N= 2886 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.318 C 0.182 G 0.182 T 0.318 Background letter frequencies (from file dataset with add-one prior applied): A 0.318 C 0.182 G 0.182 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAACCCTAAWT MEME-1 width = 11 sites = 2811 llr = 28142 E-value = 2.7e-773 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAACCCTAAWT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7991:::a742 pos.-specific C :::9aa:::12 probability G 1:1:::::2:1 matrix T 21::::a::56 bits 2.5 ** 2.2 ** 2.0 ** 1.7 ***** Relative 1.5 ***** Entropy 1.2 ******* (14.4 bits) 1.0 ******** 0.7 ******** 0.5 ********* 0.2 *********** 0.0 ----------- Multilevel AAACCCTAATT consensus GAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACCCTAAWT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 553812 bayes= 9.49395 E= 2.7e-773 122 -270 -174 -83 154 -1810 -1810 -203 156 -1810 -167 -528 -141 227 -668 -1810 -980 246 -1810 -980 -1810 246 -1810 -1810 -748 -1810 -1810 165 165 -1810 -1810 -580 122 -391 37 -463 23 -92 -251 65 -42 -28 -170 81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACCCTAAWT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2811 E= 2.7e-773 0.738883 0.028104 0.054429 0.178584 0.922092 0.000000 0.000000 0.077908 0.934543 0.000000 0.057275 0.008182 0.119886 0.878335 0.001779 0.000000 0.000356 0.999289 0.000000 0.000356 0.000000 1.000000 0.000000 0.000000 0.001779 0.000000 0.000000 0.998221 0.994308 0.000000 0.000000 0.005692 0.739239 0.012095 0.235859 0.012807 0.372821 0.096407 0.032017 0.498755 0.237638 0.150125 0.056208 0.556030 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAACCCTAAWT MEME-1 regular expression -------------------------------------------------------------------------------- AAACCCTA[AG][TA][TA] -------------------------------------------------------------------------------- Time 117.90 secs. ******************************************************************************** ******************************************************************************** MOTIF AAMCCTAR MEME-2 width = 8 sites = 2100 llr = 17135 E-value = 5.1e-168 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAMCCTAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 884:::a6 pos.-specific C ::6aa::: probability G :2:::::3 matrix T 2::::a:: bits 2.5 ** 2.2 ** 2.0 ** 1.7 ** Relative 1.5 **** Entropy 1.2 ***** (11.8 bits) 1.0 ******* 0.7 ******* 0.5 ******** 0.2 ******** 0.0 -------- Multilevel AACCCTAA consensus T A G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAMCCTAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 562470 bayes= 10.22 E= 5.1e-168 132 -1768 -1768 -62 136 -512 -4 -1768 20 180 -1768 -1768 -1768 246 -1768 -1768 -1768 246 -1768 -1768 -1768 -388 -1768 164 161 -247 -1768 -1768 93 -228 80 -292 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAMCCTAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2100 E= 5.1e-168 0.793810 0.000000 0.000000 0.206190 0.817143 0.005238 0.177619 0.000000 0.365238 0.634762 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.012381 0.000000 0.987619 0.967143 0.032857 0.000000 0.000000 0.603810 0.037619 0.316667 0.041905 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAMCCTAR MEME-2 regular expression -------------------------------------------------------------------------------- [AT]A[CA]CCTA[AG] -------------------------------------------------------------------------------- Time 226.28 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************