******************************************************************************** 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/AT1G68320_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/AT1G68320_peak_sequences.fasta -dna -oc out/AT1G68320 -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= 1479 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= 219867 N= 1479 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.331 C 0.169 G 0.169 T 0.331 Background letter frequencies (from file dataset with add-one prior applied): A 0.332 C 0.168 G 0.168 T 0.332 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAAGTTAGGYA MEME-1 width = 11 sites = 1416 llr = 11138 E-value = 1.7e-554 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAAGTTAGGYA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4563::7:::5 pos.-specific C 11:::::::42 probability G 1127:::aa:2 matrix T 3221aa3::62 bits 2.6 ** 2.3 ** 2.1 ** 1.8 ** Relative 1.5 * ** Entropy 1.3 ** ** (11.3 bits) 1.0 *** *** 0.8 *** *** 0.5 ******** 0.3 ********* 0.0 ----------- Multilevel AAAGTTAGGTA consensus TT A T CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGTTAGGYA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 205077 bayes= 8.71163 E= 1.7e-554 37 -49 -24 -10 70 -105 -21 -52 95 -789 15 -96 -26 -1711 199 -256 -1711 -1711 -211 153 -1711 -1711 -1711 159 98 -196 -357 -20 -1711 -1711 257 -1711 -1711 -1711 257 -1711 -1711 115 -357 89 46 27 -7 -87 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGTTAGGYA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1416 E= 1.7e-554 0.427966 0.119350 0.142655 0.310028 0.540960 0.081215 0.145480 0.232345 0.641949 0.000706 0.186441 0.170904 0.276836 0.000000 0.666667 0.056497 0.000000 0.000000 0.038842 0.961158 0.000000 0.000000 0.000000 1.000000 0.653249 0.043079 0.014124 0.289548 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.372175 0.014124 0.613701 0.456215 0.201977 0.160311 0.181497 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAGTTAGGYA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT]A[GA]TT[AT]GG[TC][AC] -------------------------------------------------------------------------------- Time 125.57 secs. ******************************************************************************** ******************************************************************************** MOTIF ACCRAACCRAACCAA MEME-2 width = 15 sites = 138 llr = 1733 E-value = 3.5e-054 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACCRAACCRAACCAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 8::498114883358 pos.-specific C 2aa:::881:1772: probability G :::611::51:::32 matrix T :::::121:::1::: bits 2.6 * 2.3 ** 2.1 ** 1.8 ** Relative 1.5 ** * Entropy 1.3 **** ** ** (18.1 bits) 1.0 **** ** *** 0.8 ************* * 0.5 *************** 0.3 *************** 0.0 --------------- Multilevel ACCGAACCGAACCAA consensus A A AAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCRAACCRAACCAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 199161 bayes= 12.6585 E= 3.5e-054 126 -14 -195 -551 -1375 257 -1375 -1375 -1375 253 -453 -393 15 -1375 191 -1375 144 -1375 -73 -1375 135 -221 -173 -235 -193 217 -1375 -106 -193 225 -1375 -152 31 -107 160 -1375 126 -195 -36 -352 133 -45 -221 -551 -35 204 -1375 -271 -16 205 -1375 -551 69 -1 64 -320 125 -353 -7 -320 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCRAACCRAACCAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 138 E= 3.5e-054 0.797101 0.152174 0.043478 0.007246 0.000000 1.000000 0.000000 0.000000 0.000000 0.971014 0.007246 0.021739 0.369565 0.000000 0.630435 0.000000 0.898551 0.000000 0.101449 0.000000 0.847826 0.036232 0.050725 0.065217 0.086957 0.753623 0.000000 0.159420 0.086957 0.797101 0.000000 0.115942 0.413043 0.079710 0.507246 0.000000 0.797101 0.043478 0.130435 0.028986 0.833333 0.123188 0.036232 0.007246 0.260870 0.688406 0.000000 0.050725 0.297101 0.695652 0.000000 0.007246 0.536232 0.166667 0.260870 0.036232 0.789855 0.014493 0.159420 0.036232 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACCRAACCRAACCAA MEME-2 regular expression -------------------------------------------------------------------------------- ACC[GA]AACC[GA]AA[CA][CA][AG]A -------------------------------------------------------------------------------- Time 230.34 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************