******************************************************************************** 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/AT1G80840_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/AT1G80840_peak_sequences.fasta -dna -oc out/AT1G80840 -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= 3728 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= 711564 N= 3728 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.325 C 0.175 G 0.175 T 0.325 Background letter frequencies (from file dataset with add-one prior applied): A 0.326 C 0.174 G 0.174 T 0.326 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HAARGTCAAVV MEME-1 width = 11 sites = 3694 llr = 29621 E-value = 5.6e-463 ******************************************************************************** -------------------------------------------------------------------------------- Motif HAARGTCAAVV MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4567:::aa43 pos.-specific C 221:::a::32 probability G 1113a::::24 matrix T 223::a:::11 bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Relative 1.5 ***** Entropy 1.3 ***** (11.6 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ********** 0.0 ----------- Multilevel AAAAGTCAAAG consensus CTTG CA sequence T C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAARGTCAAVV MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 674284 bayes= 9.19513 E= 5.6e-463 40 37 -52 -54 68 -4 -72 -69 90 -117 -156 -35 102 -1849 97 -1849 -1849 -1849 251 -523 -677 -1849 -1849 161 -1849 252 -1849 -1849 161 -468 -1849 -1849 160 -633 -524 -599 14 98 12 -159 -7 25 102 -134 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAARGTCAAVV MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 3694 E= 5.6e-463 0.430157 0.224418 0.121278 0.224147 0.524093 0.168652 0.105306 0.201949 0.608284 0.077152 0.059015 0.255550 0.659448 0.000000 0.340552 0.000000 0.000000 0.000000 0.991337 0.008663 0.002978 0.000000 0.000000 0.997022 0.000000 1.000000 0.000000 0.000000 0.993232 0.006768 0.000000 0.000000 0.988089 0.002166 0.004602 0.005143 0.358960 0.343259 0.189226 0.108554 0.310233 0.207363 0.353546 0.128858 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HAARGTCAAVV MEME-1 regular expression -------------------------------------------------------------------------------- [ACT][AT][AT][AG]GTCAA[AC][GAC] -------------------------------------------------------------------------------- Time 123.14 secs. ******************************************************************************** ******************************************************************************** MOTIF RGTCAA MEME-2 width = 6 sites = 2172 llr = 16485 E-value = 4.6e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGTCAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5:::aa pos.-specific C :::a:: probability G 5a:::: matrix T ::a::: bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Relative 1.5 ***** Entropy 1.3 ***** (11.0 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ****** 0.0 ------ Multilevel AGTCAA consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGTCAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 6 n= 692924 bayes= 10.333 E= 4.6e-037 65 -1773 148 -946 -1773 -1773 252 -1773 -1773 -1773 -1773 162 -1773 252 -1773 -1773 162 -1773 -1773 -1773 162 -1773 -1773 -1773 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGTCAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 6 nsites= 2172 E= 4.6e-037 0.513352 0.000000 0.486188 0.000460 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGTCAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG]GTCAA -------------------------------------------------------------------------------- Time 232.26 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************