******************************************************************************** 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/AT5G66300_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/AT5G66300_peak_sequences.fasta -dna -oc out/AT5G66300 -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= 4261 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= 992782 N= 4261 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.322 C 0.178 G 0.178 T 0.322 Background letter frequencies (from file dataset with add-one prior applied): A 0.323 C 0.177 G 0.177 T 0.323 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTDCTTNWWHYWYAMGYW MEME-1 width = 18 sites = 4236 llr = 35236 E-value = 1.5e-248 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTDCTTNWWHYWYAMGYW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 122:::2332231a6:23 pos.-specific C ::2a::3223225:4:32 probability G :14:1:3111121::91: matrix T 972:8a2444444::144 bits 2.5 2.3 * 2.0 * 1.8 * * Relative 1.5 * * * * Entropy 1.3 * * * * (12.0 bits) 1.0 * *** *** 0.8 * *** *** 0.5 ** *** **** 0.3 ******* ****** 0.0 ------------------ Multilevel TTGCTTGTTTTTCAAGTT consensus T CAACCAT C CA sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTDCTTNWWHYWYAMGYW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 920345 bayes= 9.59078 E= 1.5e-248 -159 -855 -755 146 -107 -195 -77 111 -47 -15 107 -45 -371 243 -954 -376 -1869 -415 -29 139 -496 -1869 -393 160 -85 71 98 -80 7 -3 -40 13 -19 1 -31 29 -68 70 -34 19 -74 44 -49 45 -37 5 -21 36 -192 143 -135 19 159 -315 -1869 -603 84 125 -722 -1869 -398 -1869 232 -169 -101 82 -94 43 11 10 -283 44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTDCTTNWWHYWYAMGYW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 4236 E= 1.5e-248 0.107649 0.000472 0.000944 0.890935 0.153683 0.045562 0.103399 0.697356 0.233239 0.159348 0.369924 0.237488 0.024788 0.951133 0.000236 0.023843 0.000000 0.009915 0.144712 0.845373 0.010387 0.000000 0.011568 0.978045 0.179178 0.288244 0.347262 0.185316 0.339235 0.172568 0.133617 0.354580 0.282814 0.178234 0.142351 0.396601 0.202550 0.287299 0.139991 0.370161 0.193815 0.239377 0.126062 0.440746 0.250472 0.182720 0.152738 0.414070 0.085458 0.476629 0.069169 0.368744 0.975212 0.019830 0.000000 0.004958 0.579320 0.419500 0.001180 0.000000 0.020538 0.000000 0.879367 0.100094 0.160765 0.311143 0.092304 0.435788 0.348442 0.189330 0.024788 0.437441 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTDCTTNWWHYWYAMGYW MEME-1 regular expression -------------------------------------------------------------------------------- TT[GTA]CTT[GC][TA][TA][TCA][TC][TA][CT]A[AC]G[TC][TA] -------------------------------------------------------------------------------- Time 70.67 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTYTYTTTTTYTYTTTBTTT MEME-2 width = 21 sites = 1242 llr = 11995 E-value = 6.7e-041 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTYTYTTTTTYTYTTTBTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::2:::1::::::::::322 pos.-specific C 133313:23323:43214:22 probability G :11:1211:::112:112112 matrix T 766585867785947783655 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 * (13.9 bits) 1.0 * *** * * 0.8 * * * *** * **** 0.5 *** ************** 0.3 ********************* 0.0 --------------------- Multilevel TTTTTTTTTTTTTTTTTCTTT consensus CCC C CCCCC CC TAC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTYTTTTTYTYTTTBTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 907562 bayes= 11.7622 E= 6.7e-041 -120 -124 -202 120 -1692 83 -109 90 -406 75 -104 89 -91 65 -222 67 -319 -42 -175 127 -313 92 -8 51 -413 -302 -66 139 -254 49 -108 92 -1692 68 -1692 115 -1692 52 -1692 121 -865 46 -1692 123 -365 91 -52 68 -1692 -519 -75 146 -548 107 -3 47 -1692 57 -1692 119 -1692 -12 -101 121 -1692 -34 -75 123 -1692 134 44 -4 -36 -187 -98 92 -72 47 -144 61 -110 18 6 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTYTTTTTYTYTTTBTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1242 E= 6.7e-041 0.140902 0.074879 0.043478 0.740741 0.000000 0.314010 0.082931 0.603060 0.019324 0.297101 0.086151 0.597424 0.172303 0.276167 0.037842 0.513688 0.035427 0.132045 0.052335 0.780193 0.037037 0.334944 0.167472 0.460548 0.018519 0.021739 0.111916 0.847826 0.055556 0.248792 0.083736 0.611916 0.000000 0.282609 0.000000 0.717391 0.000000 0.253623 0.000000 0.746377 0.000805 0.243156 0.000000 0.756039 0.025765 0.332528 0.123188 0.518519 0.000000 0.004831 0.104670 0.890499 0.007246 0.371176 0.173108 0.448470 0.000000 0.262480 0.000000 0.737520 0.000000 0.162641 0.087762 0.749597 0.000000 0.139291 0.104670 0.756039 0.000000 0.446055 0.239936 0.314010 0.252013 0.048309 0.089372 0.610306 0.196457 0.244767 0.065217 0.493559 0.150564 0.199678 0.184380 0.465378 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTYTTTTTYTYTTTBTTT MEME-2 regular expression -------------------------------------------------------------------------------- T[TC][TC][TC]T[TC]T[TC][TC][TC][TC][TC]T[TC][TC]TT[CTG][TA][TC]T -------------------------------------------------------------------------------- Time 134.47 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************