******************************************************************************** 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/AT5G66700_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/AT5G66700_peak_sequences.fasta -dna -oc out/AT5G66700 -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= 6554 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= 1545385 N= 6554 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.375 C 0.125 G 0.125 T 0.375 Background letter frequencies (from file dataset with add-one prior applied): A 0.376 C 0.124 G 0.124 T 0.376 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AATWATTGDWD MEME-1 width = 11 sites = 6537 llr = 45877 E-value = 1.6e-168 ******************************************************************************** -------------------------------------------------------------------------------- Motif AATWATTGDWD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 8a:4a::1332 pos.-specific C 1:::::::112 probability G :::::::8312 matrix T 1:a5:aa1344 bits 3.0 2.7 2.4 2.1 Relative 1.8 * Entropy 1.5 ** **** (10.1 bits) 1.2 ** **** 0.9 ** **** 0.6 *** **** 0.3 ********* 0.0 ----------- Multilevel AATTATTGGTT consensus A TAA sequence A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATWATTGDWD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1479845 bayes= 10.0344 E= 1.6e-168 104 -60 -808 -138 141 -966 -1932 -1932 -1932 -1932 -1932 141 12 -502 -156 54 141 -1932 -1932 -1932 -1932 -1932 -1932 141 -1932 -1932 -1932 141 -222 -1932 275 -219 -36 -65 139 -31 -34 12 14 20 -69 47 76 3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATWATTGDWD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6537 E= 1.6e-168 0.773902 0.081689 0.000459 0.143950 0.999847 0.000153 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.408903 0.003824 0.042068 0.545204 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.080924 0.000000 0.836622 0.082454 0.292489 0.079394 0.325073 0.303044 0.297843 0.134771 0.136913 0.430473 0.232981 0.172250 0.210035 0.384733 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATWATTGDWD MEME-1 regular expression -------------------------------------------------------------------------------- AAT[TA]ATTG[GTA][TA][TAG] -------------------------------------------------------------------------------- Time 73.87 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCATTTAATTTGATGGGTTGAGTTGTTAAATGGRTTAACC MEME-2 width = 41 sites = 9 llr = 453 E-value = 4.7e-019 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCATTTAATTTGATGGGTTGAGTTGTTAAATGGRTTAACC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::a:::aa:::2a:::1:::a1:::::aaa::23::aa:: pos.-specific C a:a:::::::::::::::1::::::::::::::::::::98 probability G ::::::::::::8::aa8::a:9::a::::::a87::::1: matrix T :a::aaa::aaa::a::19a:::aa:aa:::a:::aa:::2 bits 3.0 * * ** * * * 2.7 * * ** * * * 2.4 * * ** * * * * * 2.1 * * ** * * * * * Relative 1.8 * * * *** * * * ** ** Entropy 1.5 ****************** ********************** (72.6 bits) 1.2 ***************************************** 0.9 ***************************************** 0.6 ***************************************** 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel CTCATTTAATTTGATGGGTTGAGTTGTTAAATGGGTTAACC consensus A AA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCATTTAATTTGATGGGTTGAGTTGTTAAATGGRTTAACC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 1283225 bayes= 17.9694 E= 4.7e-019 -982 301 -982 -982 -982 -982 -982 141 -982 301 -982 -982 141 -982 -982 -982 -982 -982 -982 141 -982 -982 -982 141 -982 -982 -982 141 141 -982 -982 -982 141 -982 -982 -982 -982 -982 -982 141 -982 -982 -982 141 -982 -982 -982 141 -76 -982 265 -982 141 -982 -982 -982 -982 -982 -982 141 -982 -982 301 -982 -982 -982 301 -982 -175 -982 265 -175 -982 -16 -982 124 -982 -982 -982 141 -982 -982 301 -982 141 -982 -982 -982 -175 -982 284 -982 -982 -982 -982 141 -982 -982 -982 141 -982 -982 301 -982 -982 -982 -982 141 -982 -982 -982 141 141 -982 -982 -982 141 -982 -982 -982 141 -982 -982 -982 -982 -982 -982 141 -982 -982 301 -982 -76 -982 265 -982 -17 -982 242 -982 -982 -982 -982 141 -982 -982 -982 141 141 -982 -982 -982 141 -982 -982 -982 -982 284 -16 -982 -982 265 -982 -76 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCATTTAATTTGATGGGTTGAGTTGTTAAATGGRTTAACC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 9 E= 4.7e-019 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.222222 0.000000 0.777778 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.111111 0.000000 0.777778 0.111111 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.222222 0.000000 0.777778 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.111111 0.000000 0.000000 0.777778 0.000000 0.222222 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCATTTAATTTGATGGGTTGAGTTGTTAAATGGRTTAACC MEME-2 regular expression -------------------------------------------------------------------------------- CTCATTTAATTT[GA]ATGGGTTGAGTTGTTAAATG[GA][GA]TTAAC[CT] -------------------------------------------------------------------------------- Time 140.72 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************