******************************************************************************** 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/AT4G25480_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/AT4G25480_peak_sequences.fasta -dna -oc out/AT4G25480 -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= 5775 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= 1194142 N= 5775 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.299 C 0.201 G 0.201 T 0.299 Background letter frequencies (from file dataset with add-one prior applied): A 0.302 C 0.198 G 0.198 T 0.302 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YYRCCGACAW MEME-1 width = 10 sites = 5720 llr = 48928 E-value = 5.7e-546 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYRCCGACAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 215:::a:53 pos.-specific C 34:aa::a11 probability G 125::a::21 matrix T 53::::::24 bits 2.3 ** * 2.1 *** * 1.9 *** * 1.6 ***** Relative 1.4 ***** Entropy 1.2 ***** (12.3 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ********* 0.0 ---------- Multilevel TCACCGACAT consensus CTG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYRCCGACAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1142167 bayes= 9.72418 E= 5.7e-546 -88 45 -77 58 -116 101 -29 1 79 -1913 125 -563 -1913 228 -1913 -287 -1075 234 -1913 -1913 -1913 -1913 234 -1913 172 -1913 -1913 -629 -1075 234 -1913 -975 77 -64 -16 -75 11 -41 -128 55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYRCCGACAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5720 E= 5.7e-546 0.164161 0.269755 0.116084 0.450000 0.135315 0.400000 0.161538 0.303147 0.522028 0.000000 0.471853 0.006119 0.000000 0.958566 0.000000 0.041434 0.000175 0.999825 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.996154 0.000000 0.000000 0.003846 0.000175 0.999476 0.000000 0.000350 0.515909 0.127273 0.176748 0.180070 0.326049 0.148776 0.081818 0.443357 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYRCCGACAW MEME-1 regular expression -------------------------------------------------------------------------------- [TC][CT][AG]CCGACA[TA] -------------------------------------------------------------------------------- Time 79.29 secs. ******************************************************************************** ******************************************************************************** MOTIF MGRMGRMGRHGRMGRMGRAGR MEME-2 width = 21 sites = 789 llr = 9183 E-value = 3.3e-061 ******************************************************************************** -------------------------------------------------------------------------------- Motif MGRMGRMGRHGRMGRMGRAGR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3234155244145144146:5 pos.-specific C 4:24::4:12:15::3:13:1 probability G 175184185:85:95185:a4 matrix T 1112:1111311:::2::1:: bits 2.3 2.1 * 1.9 * 1.6 * * * Relative 1.4 * * * * * Entropy 1.2 * * * * * * (16.8 bits) 0.9 * * * * ** * * 0.7 * * * * *** ** ** 0.5 * ***** ***** ***** 0.2 ********************* 0.0 --------------------- Multilevel CGGCGAAGGAGGAGGAGGAGA consensus A AA GC AT AC AC AC G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGRMGRMGRHGRMGRMGRAGR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1078642 bayes= 12.7241 E= 3.3e-061 6 103 -53 -108 -78 -1627 177 -103 4 -34 119 -187 23 103 -153 -81 -154 -224 208 -431 58 -204 106 -177 62 93 -112 -212 -92 -348 193 -220 25 -186 138 -214 51 27 -200 -11 -114 -1627 204 -257 50 -173 122 -254 78 128 -1627 -1627 -181 -1627 213 -269 48 -312 143 -373 46 67 -131 -67 -110 -359 209 -1627 50 -186 138 -689 93 48 -304 -130 -350 -1627 230 -1627 74 -159 102 -350 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGRMGRMGRHGRMGRMGRAGR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 789 E= 3.3e-061 0.314322 0.405577 0.136882 0.143219 0.176172 0.000000 0.675539 0.148289 0.310520 0.155894 0.451204 0.082383 0.354880 0.404309 0.068441 0.172370 0.103929 0.041825 0.839037 0.015209 0.451204 0.048162 0.411914 0.088720 0.462611 0.376426 0.091255 0.069708 0.159696 0.017744 0.756654 0.065906 0.359949 0.054499 0.517110 0.068441 0.430925 0.239544 0.049430 0.280101 0.136882 0.000000 0.812421 0.050697 0.427123 0.059569 0.461343 0.051965 0.519645 0.480355 0.000000 0.000000 0.086185 0.000000 0.866920 0.046895 0.422053 0.022814 0.532319 0.022814 0.414449 0.315589 0.079848 0.190114 0.140684 0.016477 0.842839 0.000000 0.425856 0.054499 0.517110 0.002535 0.576679 0.276299 0.024081 0.122940 0.026616 0.000000 0.973384 0.000000 0.505703 0.065906 0.401774 0.026616 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGRMGRMGRHGRMGRMGRAGR MEME-2 regular expression -------------------------------------------------------------------------------- [CA]G[GA][CA]G[AG][AC]G[GA][ATC]G[GA][AC]G[GA][AC]G[GA][AC]G[AG] -------------------------------------------------------------------------------- Time 153.20 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************