******************************************************************************** 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/AT1G33240_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/AT1G33240_peak_sequences.fasta -dna -oc out/AT1G33240 -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= 8304 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= 2031482 N= 8304 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.365 C 0.135 G 0.135 T 0.365 Background letter frequencies (from file dataset with add-one prior applied): A 0.366 C 0.134 G 0.134 T 0.366 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAHRGTAAAA MEME-1 width = 10 sites = 8267 llr = 54304 E-value = 1.3e-084 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAHRGTAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4634::9a98 pos.-specific C 113::::::: probability G 1115a:1::: matrix T 323::a1::2 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.5 * * (9.5 bits) 1.2 ** ** 0.9 ****** 0.6 ******* 0.3 * ******* 0.0 ---------- Multilevel AAAGGTAAAA consensus T TA T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAHRGTAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1956746 bayes= 9.9387 E= 1.3e-084 27 -40 10 -23 71 -80 16 -107 -15 101 -8 -42 27 -328 192 -326 -810 -1966 290 -1966 -421 -594 -1966 142 128 -536 -139 -267 145 -1966 -653 -1966 136 -215 -1966 -373 103 -536 -811 -58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAHRGTAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 8267 E= 1.3e-084 0.442603 0.101488 0.143099 0.312810 0.598766 0.077053 0.149147 0.175033 0.329866 0.268779 0.126648 0.274707 0.440789 0.013790 0.507076 0.038345 0.001331 0.000000 0.998669 0.000000 0.019838 0.002177 0.000000 0.977985 0.887867 0.003266 0.051167 0.057699 0.998548 0.000000 0.001452 0.000000 0.942301 0.030120 0.000000 0.027580 0.750575 0.003266 0.000484 0.245676 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAHRGTAAAA MEME-1 regular expression -------------------------------------------------------------------------------- [AT]A[ATC][GA]GTAAA[AT] -------------------------------------------------------------------------------- Time 124.73 secs. ******************************************************************************** ******************************************************************************** MOTIF CGGTCCCGAGTTGGGACCAGTGTAAAAARTGAYACAAATCGATAAATTAA MEME-2 width = 50 sites = 15 llr = 806 E-value = 1.5e-015 ******************************************************************************** -------------------------------------------------------------------------------- Motif CGGTCCCGAGTTGGGACCAGTGTAAAAARTGAYACAAATCGATAAATTAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :11::::191::111a::93:1:99a9a3::a:a1aaa1:2a:999::aa pos.-specific C 81::789:1:::1:1:89:1:1::::::::::5:8::::9:::1:::::: probability G 1991:119:91:898::1:6:8:1::1:5:9::::::::18::::11::: matrix T 1:19311:::9a::1:211:a:a:1:::2a1:5:1:::9:::a:1:9a:: bits 2.9 2.6 * 2.3 * * * 2.0 ** ** * * ** * ** Relative 1.7 *** **** * *** ** * * * ** Entropy 1.5 *** **** * ******* *** * * *** ***** **** *** (77.5 bits) 1.2 **************************** ********************* 0.9 **************************** ********************* 0.6 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel CGGTCCCGAGTTGGGACCAGTGTAAAAAGTGATACAAATCGATAAATTAA consensus T T A A C A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGTCCCGAGTTGGGACCAGTGTAAAAARTGAYACAAATCGATAAATTAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 1624586 bayes= 17.9994 E= 1.5e-015 -1055 258 -100 -146 -245 -100 270 -1055 -245 -1055 270 -245 -1055 -1055 -100 135 -1055 245 -1055 -46 -1055 258 -100 -146 -1055 270 -100 -245 -146 -1055 270 -1055 135 -100 -1055 -1055 -245 -1055 280 -1055 -1055 -1055 -100 135 -1055 -1055 -1055 145 -146 -100 258 -1055 -146 -1055 270 -1055 -245 -100 258 -245 145 -1055 -1055 -1055 -1055 258 -1055 -87 -1055 270 -100 -245 135 -1055 -1055 -245 -46 0 217 -1055 -1055 -1055 -1055 145 -146 -100 258 -1055 -1055 -1055 -1055 145 124 -1055 0 -1055 135 -1055 -1055 -245 145 -1055 -1055 -1055 135 -1055 -100 -1055 145 -1055 -1055 -1055 -14 -1055 180 -87 -1055 -1055 -1055 145 -1055 -1055 280 -245 145 -1055 -1055 -1055 -1055 180 -1055 54 145 -1055 -1055 -1055 -245 258 -1055 -146 145 -1055 -1055 -1055 145 -1055 -1055 -1055 145 -1055 -1055 -1055 -245 -1055 -1055 135 -1055 280 -100 -1055 -87 -1055 258 -1055 145 -1055 -1055 -1055 -1055 -1055 -1055 145 135 -100 -1055 -1055 135 -1055 -1055 -245 135 -1055 -100 -1055 -1055 -1055 -100 135 -1055 -1055 -1055 145 145 -1055 -1055 -1055 145 -1055 -1055 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGTCCCGAGTTGGGACCAGTGTAAAAARTGAYACAAATCGATAAATTAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 15 E= 1.5e-015 0.000000 0.800000 0.066667 0.133333 0.066667 0.066667 0.866667 0.000000 0.066667 0.000000 0.866667 0.066667 0.000000 0.000000 0.066667 0.933333 0.000000 0.733333 0.000000 0.266667 0.000000 0.800000 0.066667 0.133333 0.000000 0.866667 0.066667 0.066667 0.133333 0.000000 0.866667 0.000000 0.933333 0.066667 0.000000 0.000000 0.066667 0.000000 0.933333 0.000000 0.000000 0.000000 0.066667 0.933333 0.000000 0.000000 0.000000 1.000000 0.133333 0.066667 0.800000 0.000000 0.133333 0.000000 0.866667 0.000000 0.066667 0.066667 0.800000 0.066667 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.866667 0.066667 0.066667 0.933333 0.000000 0.000000 0.066667 0.266667 0.133333 0.600000 0.000000 0.000000 0.000000 0.000000 1.000000 0.133333 0.066667 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.866667 0.000000 0.133333 0.000000 0.933333 0.000000 0.000000 0.066667 1.000000 0.000000 0.000000 0.000000 0.933333 0.000000 0.066667 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.000000 0.466667 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.933333 0.066667 1.000000 0.000000 0.000000 0.000000 0.000000 0.466667 0.000000 0.533333 1.000000 0.000000 0.000000 0.000000 0.066667 0.800000 0.000000 0.133333 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.066667 0.000000 0.000000 0.933333 0.000000 0.933333 0.066667 0.000000 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.933333 0.066667 0.000000 0.000000 0.933333 0.000000 0.000000 0.066667 0.933333 0.000000 0.066667 0.000000 0.000000 0.000000 0.066667 0.933333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CGGTCCCGAGTTGGGACCAGTGTAAAAARTGAYACAAATCGATAAATTAA MEME-2 regular expression -------------------------------------------------------------------------------- CGGT[CT]CCGAGTTGGGA[CT]CA[GA]TGTAAAAA[GAT]TGA[TC]ACAAATC[GA]ATAAATTAA -------------------------------------------------------------------------------- Time 237.54 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************