******************************************************************************** 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/AT1G79580_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/AT1G79580_peak_sequences.fasta -dna -oc out/AT1G79580 -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= 6038 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= 1339177 N= 6038 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.326 C 0.174 G 0.174 T 0.326 Background letter frequencies (from file dataset with add-one prior applied): A 0.327 C 0.173 G 0.173 T 0.327 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF BDTTDCTTNWWYTWYAMGYWA MEME-1 width = 21 sites = 5899 llr = 46585 E-value = 2.1e-312 ******************************************************************************** -------------------------------------------------------------------------------- Motif BDTTDCTTNWWYTWYAMGYWA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 231231::2332231a51146 pos.-specific C 21:119::2212224:5:42: probability G 33:13:2:3121111::71:: matrix T 33963:8a2444554::2443 bits 2.5 2.3 2.0 1.8 * Relative 1.5 * * * Entropy 1.3 * * * (11.4 bits) 1.0 * *** *** 0.8 * *** *** 0.5 * *** **** * 0.3 * ** **** * ******* 0.0 --------------------- Multilevel TTTTGCTTGTTTTTCACGTTA consensus GG A G CAACCAT ATCAT sequence A T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BDTTDCTTNWWYTWYAMGYWA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1218417 bayes= 9.89065 E= 2.1e-312 -109 2 96 4 -34 -36 81 -10 -158 -341 -482 141 -72 -133 -47 89 -24 -33 92 -34 -215 237 -767 -329 -1917 -999 49 121 -489 -899 -309 156 -63 53 101 -77 -3 -4 -54 26 -14 -35 -18 34 -71 45 -46 42 -105 42 -49 57 -34 -18 -37 47 -237 130 -73 31 157 -264 -1917 -1917 52 158 -339 -1917 -199 -1917 203 -61 -144 112 -116 38 16 13 -273 36 98 -369 -297 -3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BDTTDCTTNWWYTWYAMGYWA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5899 E= 2.1e-312 0.153924 0.175453 0.335142 0.335481 0.258688 0.134260 0.302085 0.304967 0.109680 0.016274 0.006103 0.867944 0.198508 0.068486 0.124936 0.608069 0.276827 0.137820 0.326157 0.259196 0.073911 0.891677 0.000848 0.033565 0.000000 0.000170 0.243092 0.756738 0.011019 0.000339 0.020342 0.968300 0.211731 0.249534 0.346838 0.191897 0.321410 0.168334 0.119173 0.391083 0.297678 0.135786 0.152060 0.414477 0.199695 0.236311 0.125954 0.438040 0.158162 0.231734 0.122733 0.487371 0.259027 0.152907 0.133582 0.454484 0.063401 0.426174 0.104255 0.406171 0.972199 0.027801 0.000000 0.000000 0.468045 0.515511 0.016443 0.000000 0.082387 0.000000 0.703679 0.213935 0.120698 0.375996 0.077301 0.426004 0.364977 0.189524 0.026106 0.419393 0.644177 0.013392 0.022038 0.320393 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif BDTTDCTTNWWYTWYAMGYWA MEME-1 regular expression -------------------------------------------------------------------------------- [TG][TGA]TT[GAT]C[TG]T[GCA][TA][TA][TC][TC][TA][CT]A[CA][GT][TC][TA][AT] -------------------------------------------------------------------------------- Time 124.66 secs. ******************************************************************************** ******************************************************************************** MOTIF ARAARAAGAARAARA MEME-2 width = 15 sites = 822 llr = 8853 E-value = 1.6e-014 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARAARAAGAARAARA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 75976793a94795a pos.-specific C 1::::1:::::1::: probability G 151342:7:162:5: matrix T ::::::1:::::::: bits 2.5 2.3 2.0 1.8 Relative 1.5 * Entropy 1.3 * *** * * (15.5 bits) 1.0 ** ***** *** 0.8 ********** *** 0.5 *************** 0.3 *************** 0.0 --------------- Multilevel AAAAAAAGAAGAAGA consensus G GGG A AG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARAAGAARAARA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1254645 bayes= 12.8425 E= 1.6e-014 119 -92 -53 -294 65 -1633 150 -1633 146 -1633 -76 -1633 109 -198 59 -1633 81 -515 113 -290 108 -117 33 -461 143 -229 -1633 -198 -7 -1633 200 -1633 161 -1633 -1633 -1633 142 -483 -52 -1633 43 -1633 169 -649 102 -100 45 -449 149 -1633 -206 -303 46 -1633 163 -426 154 -186 -1633 -1633 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARAAGAARAARA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 822 E= 1.6e-014 0.746959 0.091241 0.119221 0.042579 0.512165 0.000000 0.487835 0.000000 0.897810 0.000000 0.102190 0.000000 0.697080 0.043796 0.259124 0.000000 0.574209 0.004866 0.377129 0.043796 0.692214 0.076642 0.217762 0.013382 0.881995 0.035280 0.000000 0.082725 0.311436 0.000000 0.688564 0.000000 1.000000 0.000000 0.000000 0.000000 0.873479 0.006083 0.120438 0.000000 0.440389 0.000000 0.555961 0.003650 0.663017 0.086375 0.236010 0.014599 0.918491 0.000000 0.041363 0.040146 0.450122 0.000000 0.532847 0.017032 0.952555 0.047445 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARAAGAARAARA MEME-2 regular expression -------------------------------------------------------------------------------- A[AG]A[AG][AG][AG]A[GA]AA[GA][AG]A[GA]A -------------------------------------------------------------------------------- Time 229.11 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************