******************************************************************************** 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/AT3G49530_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/AT3G49530_peak_sequences.fasta -dna -oc out/AT3G49530 -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= 3785 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= 815050 N= 3785 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 0.328 C 0.172 G 0.172 T 0.328 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDTWDCTTRNNRRNKAAGNAA MEME-1 width = 21 sites = 2915 llr = 27897 E-value = 2.8e-396 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDTWDCTTRNNRRNKAAGNAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34334:::5333531aa:367 pos.-specific C 21::2a::1221122:::21: probability G 33:12:::3334324::a2:: matrix T 23653:aa1222233:::222 bits 2.5 2.3 * * 2.0 * * 1.8 * * Relative 1.5 *** *** Entropy 1.3 *** *** (13.8 bits) 1.0 *** *** 0.8 *** *** 0.5 *** *** * 0.3 ** **** ** **** ** 0.0 --------------------- Multilevel GATTACTTAAAGAAGAAGAAA consensus ATAAT GGGAGTT TTT sequence TG CT G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDTWDCTTRNNRRNKAAGNAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 739350 bayes= 10.2761 E= 2.8e-396 -13 -16 91 -55 9 -88 66 -20 -15 -191 -235 93 -5 -191 -83 72 14 -7 18 -22 -373 251 -1815 -1815 -1815 -1815 -207 155 -620 -896 -1815 160 56 -23 89 -263 -12 23 81 -75 -7 8 63 -44 4 -91 122 -93 62 -146 69 -108 -8 13 26 -16 -142 -7 126 -12 161 -1815 -797 -1815 161 -1815 -896 -990 -1815 -1815 251 -369 8 5 47 -46 90 -72 -200 -45 114 -240 -211 -70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDTWDCTTRNNRRNKAAGNAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2915 E= 2.8e-396 0.300858 0.153688 0.321784 0.223671 0.350257 0.093310 0.270326 0.286106 0.295712 0.045626 0.033619 0.625043 0.316295 0.045626 0.096398 0.541681 0.361235 0.163293 0.194168 0.281304 0.024700 0.975300 0.000000 0.000000 0.000000 0.000000 0.040823 0.959177 0.004460 0.000343 0.000000 0.995197 0.483705 0.146141 0.316981 0.053173 0.302916 0.201715 0.299828 0.195540 0.312178 0.180789 0.265523 0.241509 0.336878 0.091252 0.399657 0.172213 0.504974 0.062436 0.277187 0.155403 0.311492 0.188336 0.205489 0.294683 0.122813 0.163293 0.411664 0.302230 0.999314 0.000000 0.000686 0.000000 0.999314 0.000000 0.000343 0.000343 0.000000 0.000000 0.974614 0.025386 0.347170 0.177358 0.237050 0.238422 0.612007 0.104288 0.042882 0.240823 0.724871 0.032590 0.039794 0.202744 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDTWDCTTRNNRRNKAAGNAA MEME-1 regular expression -------------------------------------------------------------------------------- [GAT][ATG][TA][TA][AT]CTT[AG][AGC][AGT][GA][AG][ATG][GT]AAG[ATG][AT][AT] -------------------------------------------------------------------------------- Time 68.87 secs. ******************************************************************************** ******************************************************************************** MOTIF RAAGAARAARAARAARARRAA MEME-2 width = 21 sites = 942 llr = 9427 E-value = 4.9e-029 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAGAARAARAARAARARRAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 577397578496568486666 pos.-specific C 1111::::2::1111:11:11 probability G 32161242:5:343:513332 matrix T 1:1::111::::11:::::11 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 * (14.4 bits) 1.0 ** ** * 0.8 * **** **** *** * 0.5 ****************** 0.3 ********************* 0.0 --------------------- Multilevel AAAGAAAAAGAAAAAGAAAAA consensus GG A GGG A GGG A GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAGAARAARAARAARARRAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 739350 bayes= 11.8897 E= 4.9e-029 63 -115 71 -130 105 -121 52 -1652 109 -31 -91 -221 -24 -36 178 -1652 144 -1652 -68 -1652 106 -1652 52 -219 64 -417 128 -237 100 -184 38 -216 125 -4 -575 -275 41 -198 160 -1652 147 -201 -269 -395 88 -41 62 -1652 52 -127 119 -234 88 -117 61 -255 129 -62 -188 -310 43 -264 163 -1652 122 -101 -30 -510 85 -166 92 -337 95 -225 94 -1652 76 -37 56 -252 76 -45 19 -142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAGAARAARAARAARARRAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 942 E= 4.9e-029 0.508493 0.077495 0.280255 0.133758 0.679406 0.074310 0.246285 0.000000 0.699575 0.138004 0.091295 0.071125 0.278132 0.133758 0.588110 0.000000 0.892781 0.000000 0.107219 0.000000 0.682590 0.000000 0.245223 0.072187 0.510616 0.009554 0.416136 0.063694 0.656051 0.047771 0.222930 0.073248 0.781316 0.166667 0.003185 0.048832 0.435244 0.043524 0.521231 0.000000 0.909766 0.042463 0.026539 0.021231 0.606157 0.129512 0.264331 0.000000 0.471338 0.071125 0.392781 0.064756 0.605096 0.076433 0.262208 0.056263 0.803609 0.111465 0.046709 0.038217 0.441614 0.027601 0.530786 0.000000 0.766454 0.084926 0.139066 0.009554 0.590234 0.054140 0.323779 0.031847 0.633758 0.036093 0.330149 0.000000 0.556263 0.132696 0.253715 0.057325 0.555202 0.125265 0.196391 0.123142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAGAARAARAARAARARRAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG]A[GA]A[AG][AG][AG]A[GA]A[AG][AG][AG]A[GA]A[AG][AG][AG]A -------------------------------------------------------------------------------- Time 130.74 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************