******************************************************************************** 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/AT2G47070_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/AT2G47070_peak_sequences.fasta -dna -oc out/AT2G47070 -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= 2942 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= 575738 N= 2942 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.317 C 0.183 G 0.183 T 0.317 Background letter frequencies (from file dataset with add-one prior applied): A 0.32 C 0.18 G 0.18 T 0.32 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NDTCCGTACAWDW MEME-1 width = 13 sites = 2940 llr = 21564 E-value = 4.0e-308 ******************************************************************************** -------------------------------------------------------------------------------- Motif NDTCCGTACAWDW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 23321::a:5433 pos.-specific C 21:67:::a1122 probability G 231::a:::2121 matrix T 43621:a::2344 bits 2.5 * * 2.2 * * 2.0 * * 1.7 ** * Relative 1.5 **** Entropy 1.2 **** (10.6 bits) 1.0 ****** 0.7 ****** 0.5 ****** 0.2 ******* 0.0 ------------- Multilevel TTTCCGTACAATT consensus GAA TAA sequence CG A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NDTCCGTACAWDW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 540434 bayes= 9.06149 E= 4.0e-308 -64 19 25 22 -26 -34 48 9 -31 -244 -90 94 -103 185 -605 -73 -119 201 -234 -170 -987 -1817 247 -642 -1817 -673 -1817 164 164 -705 -1817 -671 -1817 246 -746 -563 62 -28 0 -84 27 -27 -55 9 -18 -4 1 18 -32 -2 -51 46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NDTCCGTACAWDW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 2940 E= 4.0e-308 0.205442 0.206122 0.214966 0.373469 0.267007 0.142857 0.250680 0.339456 0.258503 0.033333 0.096599 0.611565 0.156463 0.648299 0.002721 0.192517 0.140136 0.725510 0.035714 0.098639 0.000340 0.000000 0.995918 0.003741 0.000000 0.001701 0.000000 0.998299 0.995578 0.001361 0.000000 0.003061 0.000000 0.992517 0.001020 0.006463 0.492517 0.148299 0.180272 0.178912 0.386735 0.149660 0.122789 0.340816 0.281633 0.175170 0.181633 0.361565 0.255782 0.177211 0.126871 0.440136 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NDTCCGTACAWDW MEME-1 regular expression -------------------------------------------------------------------------------- [TGCA][TAG][TA]CCGTACA[AT][TA][TA] -------------------------------------------------------------------------------- Time 76.26 secs. ******************************************************************************** ******************************************************************************** MOTIF AARAARAARAARAARAARAAA MEME-2 width = 21 sites = 404 llr = 4474 E-value = 3.4e-041 ******************************************************************************** -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 655885884a65976773877 pos.-specific C :211:::11:1::1::121:: probability G 224225215:34124215:32 matrix T 21:::::1::::::::111:1 bits 2.5 2.2 2.0 1.7 Relative 1.5 * Entropy 1.2 * (16.0 bits) 1.0 *** * * * * 0.7 ************** *** 0.5 ******************* 0.2 ********************* 0.0 --------------------- Multilevel AAAAAAAAGAAAAAAAAGAAA consensus GGG G A GG GGG A GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 516898 bayes= 12.533 E= 3.4e-041 86 -202 21 -93 71 -19 24 -162 62 -35 103 -1530 124 -149 -23 -355 130 -202 -12 -701 67 -1530 144 -1530 135 -1530 -21 -355 130 -149 -90 -255 16 -35 148 -1530 161 -302 -1530 -1530 94 -98 72 -1530 77 -319 111 -284 145 -1530 -106 -301 107 -106 41 -1530 85 -219 109 -1530 120 -1530 44 -401 109 -128 -76 -118 -29 -14 153 -255 135 -154 -360 -155 106 -1530 88 -1530 104 -1530 44 -169 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 404 E= 3.4e-041 0.579208 0.044554 0.207921 0.168317 0.524752 0.158416 0.212871 0.103960 0.490099 0.141089 0.368812 0.000000 0.754950 0.064356 0.153465 0.027228 0.787129 0.044554 0.165842 0.002475 0.509901 0.000000 0.490099 0.000000 0.816832 0.000000 0.155941 0.027228 0.784653 0.064356 0.096535 0.054455 0.356436 0.141089 0.502475 0.000000 0.977723 0.022277 0.000000 0.000000 0.611386 0.091584 0.297030 0.000000 0.547030 0.019802 0.388614 0.044554 0.873762 0.000000 0.086634 0.039604 0.673267 0.086634 0.240099 0.000000 0.576733 0.039604 0.383663 0.000000 0.735149 0.000000 0.245050 0.019802 0.678218 0.074257 0.106436 0.141089 0.262376 0.163366 0.519802 0.054455 0.814356 0.061881 0.014851 0.108911 0.668317 0.000000 0.331683 0.000000 0.655941 0.000000 0.245050 0.099010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARAAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG][AG]AA[AG]AA[GA]A[AG][AG]A[AG][AG][AG]A[GA]A[AG][AG] -------------------------------------------------------------------------------- Time 144.25 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************