******************************************************************************** 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/AT5G67580_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/AT5G67580_peak_sequences.fasta -dna -oc out/AT5G67580 -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= 1181 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= 143647 N= 1181 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.324 C 0.176 G 0.176 T 0.324 Background letter frequencies (from file dataset with add-one prior applied): A 0.325 C 0.175 G 0.175 T 0.325 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AWTTAGGGYTW MEME-1 width = 11 sites = 1060 llr = 9813 E-value = 3.1e-1061 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWTTAGGGYTW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 65::a::::33 pos.-specific C 1:1:::::4:1 probability G 21:::aa9::: matrix T 238a:::1675 bits 2.5 ** 2.3 ** 2.0 ** 1.8 *** Relative 1.5 ***** Entropy 1.3 ***** (13.4 bits) 1.0 ******* 0.8 ******** 0.5 ******** 0.3 *********** 0.0 ----------- Multilevel AATTAGGGTTT consensus TT CAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTTAGGGYTW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 131837 bayes= 8.30062 E= 3.1e-1061 85 -149 -20 -70 66 -258 -49 5 -452 -31 -522 137 -1669 -1669 -1669 162 161 -1669 -1669 -526 -1669 -1669 251 -1669 -1669 -1669 251 -1669 -1669 -1669 229 -119 -684 117 -1669 89 -7 -595 -654 108 7 -47 -289 65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTTAGGGYTW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1060 E= 3.1e-1061 0.584906 0.062264 0.152830 0.200000 0.511321 0.029245 0.124528 0.334906 0.014151 0.141509 0.004717 0.839623 0.000000 0.000000 0.000000 1.000000 0.991509 0.000000 0.000000 0.008491 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.857547 0.142453 0.002830 0.394340 0.000000 0.602830 0.308491 0.002830 0.001887 0.686792 0.341509 0.126415 0.023585 0.508491 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWTTAGGGYTW MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT]TTAGGG[TC][TA][TA] -------------------------------------------------------------------------------- Time 74.71 secs. ******************************************************************************** ******************************************************************************** MOTIF TTAGGGTT MEME-2 width = 8 sites = 402 llr = 3828 E-value = 8.3e-187 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTAGGGTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::a::::: pos.-specific C 3:::::1: probability G :::aa9:: matrix T 7a:::19a bits 2.5 ** 2.3 ** 2.0 ** 1.8 *** Relative 1.5 ***** * Entropy 1.3 ******* (13.7 bits) 1.0 ******** 0.8 ******** 0.5 ******** 0.3 ******** 0.0 -------- Multilevel TTAGGGTT consensus C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAGGGTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 135380 bayes= 10.3176 E= 8.3e-187 -1529 67 -1529 115 -1529 -1529 -1529 162 157 -1529 -233 -1529 -1529 -1529 251 -1529 -1529 -1529 251 -1529 -1529 -1529 228 -112 -1529 -82 -1529 147 -1529 -1529 -1529 162 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAGGGTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 402 E= 8.3e-187 0.000000 0.278607 0.000000 0.721393 0.000000 0.000000 0.000000 1.000000 0.965174 0.000000 0.034826 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.850746 0.149254 0.000000 0.099502 0.000000 0.900498 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTAGGGTT MEME-2 regular expression -------------------------------------------------------------------------------- [TC]TAGGGTT -------------------------------------------------------------------------------- Time 141.23 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************