******************************************************************************** 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/AT5G13080_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/AT5G13080_peak_sequences.fasta -dna -oc out/AT5G13080 -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= 6827 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= 1495366 N= 6827 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.335 C 0.165 G 0.165 T 0.335 Background letter frequencies (from file dataset with add-one prior applied): A 0.336 C 0.164 G 0.164 T 0.336 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DYKTTGACTTTT MEME-1 width = 12 sites = 6783 llr = 58616 E-value = 5.7e-466 ******************************************************************************** -------------------------------------------------------------------------------- Motif DYKTTGACTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 321:::a::222 pos.-specific C 24:::::a2111 probability G 225::a::::12 matrix T 334aa:::8765 bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * Relative 1.6 ***** Entropy 1.3 ***** (12.5 bits) 1.0 ****** 0.8 ******* 0.5 ******* 0.3 ********** 0.0 ------------ Multilevel TCGTTGACTTTT consensus ATT AAA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYKTTGACTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 1420269 bayes= 9.97708 E= 5.7e-466 -34 -1 48 3 -95 121 -5 -22 -186 -299 163 18 -815 -487 -1937 156 -1937 -1937 -521 157 -1937 -1937 261 -1015 157 -1937 -1937 -957 -757 260 -1937 -835 -573 18 -1937 127 -58 -136 -206 100 -69 -102 -99 90 -63 -53 -10 62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYKTTGACTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 6783 E= 5.7e-466 0.266254 0.162760 0.228660 0.342326 0.174407 0.378446 0.158042 0.289105 0.092732 0.020640 0.505971 0.380658 0.001179 0.005602 0.000000 0.993218 0.000000 0.000000 0.004423 0.995577 0.000000 0.000000 0.999705 0.000295 0.999558 0.000000 0.000000 0.000442 0.001769 0.997199 0.000000 0.001032 0.006339 0.185759 0.000000 0.807902 0.224679 0.063689 0.039216 0.672416 0.208020 0.080643 0.082854 0.628483 0.216423 0.113961 0.153177 0.516438 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYKTTGACTTTT MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][CT][GT]TTGACT[TA][TA][TA] -------------------------------------------------------------------------------- Time 71.39 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARAARAARAARAARAARAARAARARAD MEME-2 width = 29 sites = 1180 llr = 12567 E-value = 3.7e-046 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAARAARARAD MEME-2 Description -------------------------------------------------------------------------------- Simplified A 67757849747757636746666537563 pos.-specific C 1:::::1:1111::1211:11::11:111 probability G 32243151142142142152242251423 matrix T ::11::::1111:12112111:2212112 bits 2.6 2.3 2.1 1.8 Relative 1.6 Entropy 1.3 (15.4 bits) 1.0 * * 0.8 * ***** * 0.5 ********* **** * * *** *** 0.3 ***************************** 0.0 ----------------------------- Multilevel AAAAAAGAAAAAAAAGAAGAAAAAGAAAG consensus GGGGG A G GGTAG AG G GATG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAARAARARAD MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 1304210 bayes= 12.2832 E= 3.7e-046 74 -95 109 -605 107 -176 38 -331 97 -295 45 -176 62 -527 132 -222 104 -601 81 -438 132 -176 -122 -296 28 -81 160 -1685 142 -224 -133 -1685 104 -84 -29 -199 32 -71 123 -181 101 -87 13 -268 112 -143 -14 -250 62 -217 129 -285 102 -1685 45 -182 77 -26 -110 -67 6 1 137 -242 89 -139 32 -160 100 -141 -90 -90 26 -207 155 -206 76 -75 50 -171 91 -27 12 -265 84 -479 126 -1685 93 -1685 10 -88 60 -88 39 -85 6 -122 149 -149 108 -1685 -91 -72 47 -117 124 -216 90 -133 17 -145 -2 -22 106 -86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAARAARARAD MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 1180 E= 3.7e-046 0.561864 0.084746 0.348305 0.005085 0.705085 0.048305 0.212712 0.033898 0.655932 0.021186 0.223729 0.099153 0.515254 0.004237 0.408475 0.072034 0.693220 0.002542 0.288136 0.016102 0.838136 0.048305 0.070339 0.043220 0.408475 0.093220 0.498305 0.000000 0.900000 0.034746 0.065254 0.000000 0.689831 0.091525 0.133898 0.084746 0.419492 0.100000 0.384746 0.095763 0.677966 0.089831 0.179661 0.052542 0.730508 0.061017 0.149153 0.059322 0.516949 0.036441 0.400000 0.046610 0.681356 0.000000 0.223729 0.094915 0.574576 0.137288 0.076271 0.211864 0.349153 0.165254 0.422881 0.062712 0.622034 0.062712 0.204237 0.111017 0.670339 0.061864 0.088136 0.179661 0.401695 0.038983 0.478814 0.080508 0.568644 0.097458 0.231356 0.102542 0.632203 0.136441 0.177966 0.053390 0.600847 0.005932 0.393220 0.000000 0.642373 0.000000 0.175424 0.182203 0.510169 0.088983 0.214407 0.186441 0.349153 0.070339 0.461017 0.119492 0.709322 0.000000 0.087288 0.203390 0.465254 0.072881 0.386441 0.075424 0.627966 0.065254 0.183898 0.122881 0.332203 0.140678 0.342373 0.184746 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAARAARARAD MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG][AG][AG][AG]A[GA]AA[AG]AA[AG][AG][AT][GA][AG]A[GA][AG]A[AG]A[AG][GA][AT][AG]A[GA] -------------------------------------------------------------------------------- Time 141.25 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************