******************************************************************************** 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/AT3G10113_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/AT3G10113_peak_sequences.fasta -dna -oc out/AT3G10113 -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= 9870 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= 2421728 N= 9870 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.376 C 0.124 G 0.124 T 0.376 Background letter frequencies (from file dataset with add-one prior applied): A 0.377 C 0.123 G 0.123 T 0.377 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGATATTTTTW MEME-1 width = 11 sites = 9849 llr = 70578 E-value = 9.1e-188 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGATATTTTTW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 6:a:7::1223 pos.-specific C ::::::::122 probability G 19::::::112 matrix T 31:a3aa9754 bits 3.0 2.7 2.4 * 2.1 * Relative 1.8 * Entropy 1.5 *** ** (10.3 bits) 1.2 *** ** 0.9 *** *** 0.6 ******* 0.3 ********* 0.0 ----------- Multilevel AGATATTTTTT consensus T T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATATTTTTW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2323028 bayes= 9.98515 E= 9.1e-188 68 -251 1 -58 -513 -1991 293 -289 141 -1991 -1991 -1185 -1991 -1991 -1991 141 95 -384 -1991 -51 -1185 -457 -1991 140 -1991 -1991 -1024 141 -252 -489 -1991 130 -96 -77 -104 84 -105 30 18 48 -46 31 59 4 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATATTTTTW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 9849 E= 9.1e-188 0.602904 0.021627 0.124277 0.251193 0.010763 0.000000 0.938572 0.050665 0.999898 0.000000 0.000000 0.000102 0.000000 0.000000 0.000000 1.000000 0.726368 0.008630 0.000000 0.265002 0.000102 0.005178 0.000000 0.994720 0.000000 0.000000 0.000102 0.999898 0.065590 0.004163 0.000000 0.930247 0.193827 0.072495 0.059905 0.673774 0.181440 0.151995 0.139608 0.526957 0.273936 0.152706 0.185400 0.387958 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATATTTTTW MEME-1 regular expression -------------------------------------------------------------------------------- [AT]GAT[AT]TTTTT[TA] -------------------------------------------------------------------------------- Time 76.05 secs. ******************************************************************************** ******************************************************************************** MOTIF ATTTATAYAATTATTAATTTATGATATTGATGRGACCATAT MEME-2 width = 41 sites = 18 llr = 713 E-value = 2.2e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATTTATAYAATTATTAATTTATGATATTGATGRGACCATAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 8:118:829a::a::aa:::9:28:a::39::4:a::a:a: pos.-specific C :1:1:1:5::::::::::1::::1::11:::::::a8:::: probability G 11::1:2:1:::::::::::1:81::::7::a6a::::::: matrix T 199829:3::aa:aa::a9a:a::a:99:1a:::::2:a:a bits 3.0 * * * 2.7 * * * 2.4 * * * 2.1 * * * Relative 1.8 * * * * ** Entropy 1.5 ********* * ** ** * ** ******** (57.1 bits) 1.2 * * *************** ***** *********** 0.9 ** ************************************ 0.6 ***************************************** 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel ATTTATACAATTATTAATTTATGATATTGATGGGACCATAT consensus T A A A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATAYAATTATTAATTTATGATATTGATGRGACCATAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 2026928 bayes= 18.1853 E= 2.2e-011 115 -1081 -115 -176 -1081 -115 -115 124 -276 -1081 -1081 133 -176 -115 -1081 115 105 -1081 -115 -118 -1081 -15 -1081 124 115 -1081 43 -1081 -118 202 -1081 -18 124 -1081 -15 -1081 141 -1081 -1081 -1081 -1081 -1081 -1081 141 -1081 -1081 -1081 141 141 -1081 -1081 -1081 -1081 -1081 -1081 141 -1081 -1081 -1081 141 141 -1081 -1081 -1081 141 -1081 -1081 -1081 -1081 -1081 -1081 141 -1081 -115 -1081 133 -1081 -1081 -1081 141 133 -1081 -115 -1081 -1081 -1081 -1081 141 -76 -1081 266 -1081 115 -15 -115 -1081 -1081 -1081 -1081 141 141 -1081 -1081 -1081 -1081 -115 -1081 133 -1081 -115 -1081 133 -44 -1081 255 -1081 124 -1081 -1081 -176 -1081 -1081 -1081 141 -1081 -1081 302 -1081 24 -1081 217 -1081 -1081 -1081 302 -1081 141 -1081 -1081 -1081 -1081 302 -1081 -1081 -1081 266 -1081 -76 141 -1081 -1081 -1081 -1081 -1081 -1081 141 141 -1081 -1081 -1081 -1081 -1081 -1081 141 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATAYAATTATTAATTTATGATATTGATGRGACCATAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 18 E= 2.2e-011 0.833333 0.000000 0.055556 0.111111 0.000000 0.055556 0.055556 0.888889 0.055556 0.000000 0.000000 0.944444 0.111111 0.055556 0.000000 0.833333 0.777778 0.000000 0.055556 0.166667 0.000000 0.111111 0.000000 0.888889 0.833333 0.000000 0.166667 0.000000 0.166667 0.500000 0.000000 0.333333 0.888889 0.000000 0.111111 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 1.000000 0.000000 0.000000 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 0.000000 0.000000 0.000000 1.000000 0.000000 0.055556 0.000000 0.944444 0.000000 0.000000 0.000000 1.000000 0.944444 0.000000 0.055556 0.000000 0.000000 0.000000 0.000000 1.000000 0.222222 0.000000 0.777778 0.000000 0.833333 0.111111 0.055556 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.055556 0.000000 0.944444 0.000000 0.055556 0.000000 0.944444 0.277778 0.000000 0.722222 0.000000 0.888889 0.000000 0.000000 0.111111 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.444444 0.000000 0.555556 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.777778 0.000000 0.222222 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATTTATAYAATTATTAATTTATGATATTGATGRGACCATAT MEME-2 regular expression -------------------------------------------------------------------------------- ATTTATA[CT]AATTATTAATTTAT[GA]ATATT[GA]ATG[GA]GAC[CT]ATAT -------------------------------------------------------------------------------- Time 138.90 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************