******************************************************************************** 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/AT1G49010_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/AT1G49010_peak_sequences.fasta -dna -oc out/AT1G49010 -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= 1885 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= 307689 N= 1885 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.333 C 0.167 G 0.167 T 0.333 Background letter frequencies (from file dataset with add-one prior applied): A 0.335 C 0.165 G 0.165 T 0.335 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAYCTTATCYWHWWH MEME-1 width = 15 sites = 1793 llr = 15019 E-value = 2.2e-583 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAYCTTATCYWHWWH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 56:1::a:::43433 pos.-specific C 1158::::a613113 probability G 11:1::::::11111 matrix T 324:99:a:443443 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.6 * *** Entropy 1.3 ** *** (12.1 bits) 1.0 ******* 0.8 ******** 0.5 ******** 0.3 ********** 0.0 --------------- Multilevel AACCTTATCCAAATA consensus TTT TTTTAT sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAYCTTATCYWHWWH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 281299 bayes= 9.42087 E= 2.2e-583 66 -64 -102 -24 85 -121 -95 -49 -302 162 -189 28 -173 225 -60 -664 -356 -289 -1745 150 -285 -300 -396 146 158 -1745 -1745 -1745 -1745 -1745 -1745 158 -1745 260 -1745 -1745 -402 175 -475 31 37 -95 -98 25 -5 68 -90 -5 42 -40 -135 12 0 -22 -90 38 -6 67 -57 -13 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAYCTTATCYWHWWH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1793 E= 2.2e-583 0.529838 0.105968 0.081428 0.282766 0.605131 0.071389 0.085332 0.238148 0.041272 0.506414 0.044618 0.407697 0.100948 0.786949 0.108756 0.003346 0.028444 0.022309 0.000000 0.949247 0.046291 0.020636 0.010597 0.922476 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.020636 0.557167 0.006135 0.416062 0.432236 0.085332 0.083659 0.398773 0.324038 0.264919 0.088678 0.322365 0.446737 0.124930 0.064696 0.363636 0.334077 0.141662 0.088678 0.435583 0.320134 0.263246 0.110987 0.305633 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAYCTTATCYWHWWH MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][CT]CTTATC[CT][AT][ATC][AT][TA][ATC] -------------------------------------------------------------------------------- Time 123.88 secs. ******************************************************************************** ******************************************************************************** MOTIF TACCCGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC MEME-2 width = 50 sites = 10 llr = 646 E-value = 6.9e-055 ******************************************************************************** -------------------------------------------------------------------------------- Motif TACCCGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :9:::1::::aa::::::::1:a::1:1:a:aa:a:::::aa:::1:::: pos.-specific C ::98a::1::::a:a::::a::::98:::::::a::::::::::a::::a probability G :1:::9a:::::::::a:::9a:::::9a:::::::a:::::::::a::: matrix T a:12:::9aa:::a:a:aa::::a11a:::a::::a:aaa::aa:9:aa: bits 2.6 * * * * * * * * * * * * * 2.3 * * * * * * * * * * * * * 2.1 * *** * * * *** * ** * * * * * 1.8 * *** * * * *** * ** * * * * * Relative 1.6 * ***** ************************************* **** Entropy 1.3 ********************************************* **** (93.2 bits) 1.0 ************************************************** 0.8 ************************************************** 0.5 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel TACCCGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCCGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 215324 bayes= 15.8681 E= 6.9e-055 -997 -997 -997 158 143 -997 -72 -997 -997 244 -997 -174 -997 227 -997 -74 -997 260 -997 -997 -174 -997 244 -997 -997 -997 260 -997 -997 -72 -997 143 -997 -997 -997 158 -997 -997 -997 158 158 -997 -997 -997 158 -997 -997 -997 -997 260 -997 -997 -997 -997 -997 158 -997 260 -997 -997 -997 -997 -997 158 -997 -997 260 -997 -997 -997 -997 158 -997 -997 -997 158 -997 260 -997 -997 -174 -997 244 -997 -997 -997 260 -997 158 -997 -997 -997 -997 -997 -997 158 -997 244 -997 -174 -174 227 -997 -174 -997 -997 -997 158 -174 -997 244 -997 -997 -997 260 -997 158 -997 -997 -997 -997 -997 -997 158 158 -997 -997 -997 158 -997 -997 -997 -997 260 -997 -997 158 -997 -997 -997 -997 -997 -997 158 -997 -997 260 -997 -997 -997 -997 158 -997 -997 -997 158 -997 -997 -997 158 158 -997 -997 -997 158 -997 -997 -997 -997 -997 -997 158 -997 -997 -997 158 -997 260 -997 -997 -174 -997 -997 143 -997 -997 260 -997 -997 -997 -997 158 -997 -997 -997 158 -997 260 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCCGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 10 E= 6.9e-055 0.000000 0.000000 0.000000 1.000000 0.900000 0.000000 0.100000 0.000000 0.000000 0.900000 0.000000 0.100000 0.000000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.100000 0.000000 0.900000 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 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.900000 0.000000 0.100000 0.100000 0.800000 0.000000 0.100000 0.000000 0.000000 0.000000 1.000000 0.100000 0.000000 0.900000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 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 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 1.000000 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 1.000000 0.000000 0.000000 0.100000 0.000000 0.000000 0.900000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TACCCGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC MEME-2 regular expression -------------------------------------------------------------------------------- TAC[CT]CGGTTTAACTCTGTTCGGATCCTGGATAACATGTTTAATTCTGTTC -------------------------------------------------------------------------------- Time 228.35 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************