******************************************************************************** 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/AT5G11510_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/AT5G11510_peak_sequences.fasta -dna -oc out/AT5G11510 -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= 2188 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= 475895 N= 2188 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.327 C 0.173 G 0.173 T 0.327 Background letter frequencies (from file dataset with add-one prior applied): A 0.329 C 0.171 G 0.171 T 0.329 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWWWTRACCGTTRND MEME-1 width = 15 sites = 2064 llr = 19106 E-value = 8.8e-499 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWWWTRACCGTTRND MEME-1 Description -------------------------------------------------------------------------------- Simplified A 45341471::::434 pos.-specific C 1:111::9a::::21 probability G 1:12142::a::532 matrix T 3453721:::aa122 bits 2.5 ** 2.3 ** 2.0 *** 1.8 *** Relative 1.5 ***** Entropy 1.3 ***** (13.4 bits) 1.0 ***** 0.8 ****** 0.5 ********* 0.3 * ********* 0.0 --------------- Multilevel AATATAACCGTTGGA consensus TTAT GG AAT sequence T TG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWTRACCGTTRND MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 445263 bayes= 9.49177 E= 8.8e-499 43 -85 -38 1 65 -199 -269 34 -2 -85 -96 58 21 -35 6 -9 -205 -72 -80 113 39 -1766 107 -64 105 -388 47 -221 -244 245 -1766 -1766 -1766 254 -1766 -1766 -1766 -1766 254 -1766 -1766 -1766 -1766 161 -1766 -1766 -1766 161 37 -477 150 -196 -21 7 85 -53 39 -73 41 -47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWTRACCGTTRND MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2064 E= 8.8e-499 0.441860 0.094961 0.131783 0.331395 0.514050 0.043120 0.026647 0.416182 0.324612 0.094961 0.088178 0.492248 0.378876 0.134205 0.178779 0.308140 0.079457 0.104167 0.098353 0.718023 0.429748 0.000000 0.359012 0.211240 0.679264 0.011628 0.237888 0.071221 0.060562 0.939438 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 1.000000 0.000000 0.000000 0.000000 1.000000 0.423934 0.006298 0.485465 0.084302 0.284399 0.180233 0.308140 0.227229 0.431686 0.103198 0.227713 0.237403 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWWWTRACCGTTRND MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][TA][AT]T[AGT][AG]CCGTT[GA][GAT][ATG] -------------------------------------------------------------------------------- Time 75.87 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARARRRAGARRRARARARA MEME-2 width = 21 sites = 382 llr = 4368 E-value = 5.6e-049 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARARRRAGARRRARARARA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 476586669396669493635 pos.-specific C :11:::::1::1:11:11111 probability G 53352344:71443:6:5251 matrix T 1:::11::1:::::1::12:2 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 ** * (16.5 bits) 1.0 ***** * *** 0.8 ** ** ******* *** 0.5 ****************** * 0.3 ********************* 0.0 --------------------- Multilevel GAAAAAAAAGAAAAAGAGAGA consensus AGGG GGG A GGG A A A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARARRRAGARRRARARARA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 432135 bayes= 12.4062 E= 5.6e-049 28 -203 154 -239 107 -171 58 -1522 89 -151 80 -339 58 -186 143 -1522 122 -1522 -1 -239 76 -223 77 -155 84 -1522 125 -597 84 -323 120 -1522 139 -128 -603 -239 -5 -1522 200 -1522 150 -403 -157 -1522 78 -113 107 -1522 80 -1522 128 -465 84 -123 87 -365 140 -128 -1522 -239 31 -1522 179 -1522 141 -57 -403 -1522 -24 -99 160 -148 79 -75 -10 -95 8 -64 155 -306 72 -33 -20 -93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARARRRAGARRRARARARA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 382 E= 5.6e-049 0.397906 0.041885 0.497382 0.062827 0.691099 0.052356 0.256545 0.000000 0.609948 0.060209 0.298429 0.031414 0.489529 0.047120 0.463351 0.000000 0.767016 0.000000 0.170157 0.062827 0.557592 0.036649 0.293194 0.112565 0.586387 0.000000 0.408377 0.005236 0.589005 0.018325 0.392670 0.000000 0.863874 0.070681 0.002618 0.062827 0.316754 0.000000 0.683246 0.000000 0.931937 0.010471 0.057592 0.000000 0.562827 0.078534 0.358639 0.000000 0.570681 0.000000 0.416230 0.013089 0.586387 0.073298 0.314136 0.026178 0.866492 0.070681 0.000000 0.062827 0.408377 0.000000 0.591623 0.000000 0.874346 0.115183 0.010471 0.000000 0.277487 0.086387 0.518325 0.117801 0.568063 0.102094 0.159686 0.170157 0.348168 0.109948 0.502618 0.039267 0.541885 0.136126 0.149215 0.172775 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARARRRAGARRRARARARA MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG][AG][AG]A[AG][AG][AG]A[GA]A[AG][AG][AG]A[GA]A[GA]A[GA]A -------------------------------------------------------------------------------- Time 136.87 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************