******************************************************************************** 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/AT1G02230_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/AT1G02230_peak_sequences.fasta -dna -oc out/AT1G02230 -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= 5916 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= 1065323 N= 5916 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.316 C 0.184 G 0.184 T 0.316 Background letter frequencies (from file dataset with add-one prior applied): A 0.318 C 0.182 G 0.182 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTTVTYHHNYAAGYW MEME-1 width = 15 sites = 5914 llr = 52191 E-value = 6.0e-685 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTVTYHHNYAAGYW MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::2112231aa:13 pos.-specific C a::4234224:::31 probability G :::3111121::a1: matrix T :aa1653423:::45 bits 2.5 * * 2.2 * * 2.0 * * 1.7 * * * Relative 1.5 *** *** Entropy 1.2 *** *** (12.7 bits) 1.0 *** *** 0.7 *** *** 0.5 *** **** 0.2 ******* ****** 0.0 --------------- Multilevel CTTCTTCTACAAGTT consensus GCCTAGT CA sequence A ACT C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTVTYHHNYAAGYW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 982499 bayes= 9.23375 E= 6.0e-685 -635 245 -1917 -1917 -1917 -708 -346 163 -741 -449 -555 164 -60 111 53 -126 -149 20 -102 89 -111 58 -51 51 -48 99 -49 -18 -38 40 -39 24 7 24 32 -52 -168 130 -83 14 165 -1007 -617 -1917 160 -250 -808 -729 -787 -708 245 -1917 -112 72 -52 42 10 -67 -261 70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTVTYHHNYAAGYW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5914 E= 6.0e-685 0.003889 0.996111 0.000000 0.000000 0.000000 0.001353 0.016571 0.982076 0.001860 0.008116 0.003889 0.986135 0.209841 0.392966 0.264288 0.132905 0.112783 0.209672 0.089956 0.587589 0.147109 0.272404 0.128340 0.452147 0.227257 0.363206 0.129523 0.280014 0.244335 0.240446 0.138992 0.376226 0.334122 0.216266 0.228103 0.221508 0.098918 0.448427 0.102807 0.349848 0.997295 0.000169 0.002536 0.000000 0.964998 0.032296 0.000676 0.002029 0.001353 0.001353 0.997295 0.000000 0.145925 0.301319 0.127494 0.425262 0.340717 0.114812 0.029929 0.514542 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTVTYHHNYAAGYW MEME-1 regular expression -------------------------------------------------------------------------------- CTT[CGA][TC][TC][CTA][TAC][AGTC][CT]AAG[TC][TA] -------------------------------------------------------------------------------- Time 129.66 secs. ******************************************************************************** ******************************************************************************** MOTIF YTCTYYTTCTTYYTY MEME-2 width = 15 sites = 1178 llr = 11620 E-value = 4.2e-035 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTCTYYTTCTTYYTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 11:::::::1::::: pos.-specific C 4:7:45217:34315 probability G ::::1:1:111:1:1 matrix T 492a55793875694 bits 2.5 2.2 2.0 1.7 Relative 1.5 * Entropy 1.2 *** * * (14.2 bits) 1.0 *** * ** * 0.7 ************** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TTCTTTTTCTTTTTC consensus C T CCC T CCC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCTYYTTCTTYYTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 982499 bayes= 12.0061 E= 4.2e-035 -163 117 -222 49 -246 -310 -1685 154 -522 200 -232 -50 -385 -1685 -1685 162 -1685 112 -170 79 -1685 140 -1685 71 -1685 33 -164 116 -438 -63 -1685 145 -430 186 -164 -28 -226 -289 -102 137 -1685 62 -187 108 -696 127 -239 72 -464 80 -131 91 -1685 -44 -1685 145 -696 157 -131 27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCTYYTTCTTYYTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1178 E= 4.2e-035 0.102716 0.410866 0.039049 0.447368 0.057725 0.021222 0.000000 0.921053 0.008489 0.730051 0.036503 0.224958 0.022071 0.000000 0.000000 0.977929 0.000000 0.396435 0.056027 0.547538 0.000000 0.480475 0.000000 0.519525 0.000000 0.230051 0.058574 0.711375 0.015280 0.117997 0.000000 0.866723 0.016129 0.664686 0.058574 0.260611 0.066214 0.024618 0.089983 0.819185 0.000000 0.280136 0.050085 0.669779 0.002547 0.440577 0.034805 0.522071 0.012733 0.318336 0.073854 0.595076 0.000000 0.134126 0.000000 0.865874 0.002547 0.540747 0.073854 0.382852 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCTYYTTCTTYYTY MEME-2 regular expression -------------------------------------------------------------------------------- [TC]T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[CT] -------------------------------------------------------------------------------- Time 241.80 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************