******************************************************************************** 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/AT3G11280_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/AT3G11280_peak_sequences.fasta -dna -oc out/AT3G11280 -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= 4064 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= 812891 N= 4064 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.34 C 0.16 G 0.16 T 0.34 Background letter frequencies (from file dataset with add-one prior applied): A 0.341 C 0.159 G 0.159 T 0.341 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DWRGATAAGRW MEME-1 width = 11 sites = 4059 llr = 29805 E-value = 7.8e-300 ******************************************************************************** -------------------------------------------------------------------------------- Motif DWRGATAAGRW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 355:a:9a143 pos.-specific C 11::::::111 probability G 323a::::651 matrix T 331::a::1:6 bits 2.7 * 2.4 * 2.1 * 1.9 * Relative 1.6 *** Entropy 1.3 *** * (10.6 bits) 1.1 ***** 0.8 ******* 0.5 ******* 0.3 ********* 0.0 ----------- Multilevel AAAGATAAGGT consensus GTG AA sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWRGATAAGRW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 772251 bayes= 9.33175 E= 7.8e-300 -8 -56 92 -35 43 -99 11 -24 64 -179 93 -152 -1863 -1863 266 -1043 154 -601 -563 -1863 -1863 -1863 -542 155 146 -408 -255 -399 153 -1863 -487 -511 -196 -22 200 -128 37 -155 157 -328 -19 -111 -135 73 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWRGATAAGRW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 4059 E= 7.8e-300 0.323971 0.107416 0.299828 0.268785 0.460705 0.079576 0.171471 0.288248 0.533629 0.045824 0.301798 0.118748 0.000000 0.000000 0.999754 0.000246 0.994334 0.002464 0.003203 0.000000 0.000000 0.000000 0.003695 0.996305 0.942104 0.009362 0.027100 0.021434 0.984725 0.000000 0.005420 0.009855 0.087460 0.136487 0.635132 0.140921 0.440010 0.054201 0.470559 0.035230 0.299581 0.073417 0.062331 0.564671 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWRGATAAGRW MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][AT][AG]GATAAG[GA][TA] -------------------------------------------------------------------------------- Time 77.31 secs. ******************************************************************************** ******************************************************************************** MOTIF HTYTTYTTYTTYYTCTYYYTY MEME-2 width = 21 sites = 989 llr = 9971 E-value = 6.4e-063 ******************************************************************************** -------------------------------------------------------------------------------- Motif HTYTTYTTYTTYYTCTYYYTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21:2::2112::2:12::21: pos.-specific C 3161352161353:7135326 probability G 1:::111:1:1:1:1:::::1 matrix T 3836745837655a2765573 bits 2.7 2.4 2.1 1.9 Relative 1.6 * Entropy 1.3 * (14.5 bits) 1.1 * * ** * 0.8 ** ** ** ** ** ** * 0.5 ***** ** ** ***** ** 0.3 ********************* 0.0 --------------------- Multilevel TTCTTCTTCTTTTTCTTCTTC consensus C TACTC T CCC TACTC T sequence A A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTTYTTYTTYYTCTYYYTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 731611 bayes= 11.7619 E= 6.4e-063 -62 106 -50 -3 -273 -29 -1659 126 -381 191 -208 0 -53 -35 -1659 90 -1659 77 -154 98 -1659 169 -132 32 -63 52 -123 50 -173 -55 -1659 121 -264 185 -162 -9 -95 -24 -244 95 -1659 93 -129 89 -1659 152 -297 62 -89 93 -146 42 -1659 -729 -1659 155 -267 206 -103 -73 -76 -75 -1659 104 -459 110 -201 83 -331 161 -254 41 -55 86 -629 49 -223 -4 -190 110 -1659 193 -88 -15 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTTYTTYTTYYTCTYYYTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 989 E= 6.4e-063 0.221436 0.331648 0.112235 0.334681 0.051567 0.129424 0.000000 0.819009 0.024267 0.596562 0.037412 0.341759 0.236603 0.124368 0.000000 0.639029 0.000000 0.269970 0.054601 0.675430 0.000000 0.510617 0.063701 0.425683 0.220425 0.227503 0.067745 0.484328 0.103134 0.108190 0.000000 0.788675 0.054601 0.573306 0.051567 0.320526 0.176946 0.134479 0.029323 0.659252 0.000000 0.302326 0.064712 0.632963 0.000000 0.456016 0.020222 0.523761 0.184024 0.302326 0.057634 0.456016 0.000000 0.001011 0.000000 0.998989 0.053589 0.663296 0.077856 0.205258 0.202224 0.094034 0.000000 0.703741 0.014156 0.339737 0.039434 0.606673 0.034378 0.485339 0.027300 0.452983 0.232558 0.287159 0.002022 0.478261 0.072801 0.154702 0.042467 0.730030 0.000000 0.605662 0.085945 0.308392 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTTYTTYTTYYTCTYYYTY MEME-2 regular expression -------------------------------------------------------------------------------- [TCA]T[CT][TA][TC][CT][TCA]T[CT]T[TC][TC][TC]T[CT][TA][TC][CT][TCA]T[CT] -------------------------------------------------------------------------------- Time 144.84 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************