******************************************************************************** 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/AT5G62470_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/AT5G62470_peak_sequences.fasta -dna -oc out/AT5G62470 -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= 2634 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= 435682 N= 2634 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.308 C 0.192 G 0.192 T 0.308 Background letter frequencies (from file dataset with add-one prior applied): A 0.31 C 0.19 G 0.19 T 0.31 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDWRKTRGTTGGDRRDTDDD MEME-1 width = 20 sites = 2583 llr = 20527 E-value = 3.3e-529 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDWRKTRGTTGGDRRDTDDD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3343114:::2224332334 pos.-specific C 111::1::::::11111111 probability G 43156:4a3:8643432333 matrix T 3342382:7a:132135322 bits 2.4 * 2.2 * 1.9 * 1.7 * * Relative 1.4 * ** Entropy 1.2 * ** (11.5 bits) 1.0 * **** 0.7 ** ***** 0.5 ********* 0.2 * *********** *** 0.0 -------------------- Multilevel GTAGGTAGTTGGGAGGTTAA consensus AATAT G G AATGATAGGG sequence TG A AGATT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDWRKTRGTTGGDRRDTDDD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 385636 bayes= 9.47217 E= 3.3e-529 -13 -107 95 -26 -5 -136 62 11 43 -155 -49 30 6 -1798 138 -77 -145 -735 155 9 -258 -78 -893 143 43 -1798 104 -70 -1798 -1798 240 -1798 -1798 -1798 43 126 -1798 -1798 -694 169 -60 -635 206 -864 -46 -202 165 -122 -56 -89 106 -9 42 -78 57 -69 4 -80 122 -126 -14 -173 85 4 -47 -145 9 70 -25 -58 51 14 5 -63 74 -37 18 -63 68 -48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDWRKTRGTTGGDRRDTDDD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 2583 E= 3.3e-529 0.282617 0.090592 0.367402 0.259388 0.299652 0.073945 0.291134 0.335269 0.417731 0.065041 0.135114 0.382114 0.324042 0.000000 0.494386 0.181572 0.113821 0.001161 0.554781 0.330236 0.051878 0.110724 0.000387 0.837011 0.418506 0.000000 0.390244 0.191250 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.255517 0.744483 0.000000 0.000000 0.001549 0.998451 0.204801 0.002323 0.792102 0.000774 0.225707 0.046845 0.594657 0.132791 0.210221 0.102207 0.395277 0.292296 0.415021 0.110724 0.282230 0.192025 0.318622 0.108788 0.442896 0.129694 0.281843 0.057298 0.342625 0.318235 0.223384 0.069299 0.201703 0.505614 0.261711 0.126984 0.270616 0.340689 0.320945 0.122726 0.317073 0.239257 0.351529 0.122338 0.303523 0.222609 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDWRKTRGTTGGDRRDTDDD MEME-1 regular expression -------------------------------------------------------------------------------- [GAT][TAG][AT][GA][GT]T[AG]G[TG]T[GA][GA][GTA][AG][GA][GTA][TAG][TGA][AGT][AGT] -------------------------------------------------------------------------------- Time 75.53 secs. ******************************************************************************** ******************************************************************************** MOTIF HGGARGAGRAGRAGRMGGAGR MEME-2 width = 21 sites = 313 llr = 3518 E-value = 8.9e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif HGGARGAGRAGRAGRMGGAGR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 413542734623524433614 pos.-specific C 31:2::1::1::1::3:::11 probability G :87267176166274277176 matrix T 3::2::1::21:1112::31: bits 2.4 2.2 1.9 1.7 Relative 1.4 * * * Entropy 1.2 ** * * ** (16.2 bits) 1.0 ** * ** ** * ** * 0.7 ** ** ** ** * ** ** 0.5 *** ***** ** ** ** ** 0.2 *** *********** ***** 0.0 --------------------- Multilevel AGGAGGAGGAGGAGGAGGAGG consensus C ATAA AATAA ACAAT A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HGGARGAGRAGRAGRMGGAGR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 383002 bayes= 12.3102 E= 8.9e-037 35 84 -1493 -23 -174 -53 203 -1493 -5 -389 186 -1493 59 -19 -34 -51 21 -308 159 -269 -32 -1493 196 -460 119 -94 -125 -143 -24 -1493 196 -1493 32 -219 158 -660 86 -53 -131 -43 -45 -1493 176 -124 14 -308 171 -428 82 -47 4 -135 -69 -209 186 -208 50 -308 122 -165 43 43 -34 -82 -23 -431 193 -660 -18 -1493 193 -660 95 -199 -131 -16 -221 -131 190 -108 18 -189 154 -279 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HGGARGAGRAGRAGRMGGAGR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 313 E= 8.9e-037 0.396166 0.338658 0.000000 0.265176 0.092652 0.130990 0.776358 0.000000 0.300319 0.012780 0.686901 0.000000 0.466454 0.166134 0.150160 0.217252 0.357827 0.022364 0.571885 0.047923 0.249201 0.000000 0.738019 0.012780 0.706070 0.099042 0.079872 0.115016 0.261981 0.000000 0.738019 0.000000 0.386581 0.041534 0.568690 0.003195 0.562300 0.130990 0.076677 0.230032 0.226837 0.000000 0.642173 0.130990 0.341853 0.022364 0.619808 0.015974 0.546326 0.137380 0.194888 0.121406 0.191693 0.044728 0.690096 0.073482 0.437700 0.022364 0.440895 0.099042 0.418530 0.255591 0.150160 0.175719 0.265176 0.009585 0.722045 0.003195 0.274760 0.000000 0.722045 0.003195 0.597444 0.047923 0.076677 0.277955 0.067093 0.076677 0.709265 0.146965 0.351438 0.051118 0.552716 0.044728 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HGGARGAGRAGRAGRMGGAGR MEME-2 regular expression -------------------------------------------------------------------------------- [ACT]G[GA][AT][GA][GA]A[GA][GA][AT][GA][GA]AG[GA][AC][GA][GA][AT]G[GA] -------------------------------------------------------------------------------- Time 136.25 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************