******************************************************************************** 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/AT5G52020_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/AT5G52020_peak_sequences.fasta -dna -oc out/AT5G52020 -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= 3642 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= 789399 N= 3642 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.294 C 0.206 G 0.206 T 0.294 Background letter frequencies (from file dataset with add-one prior applied): A 0.296 C 0.203 G 0.203 T 0.296 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HDDTGTCGGCRRHDD MEME-1 width = 15 sites = 3637 llr = 31258 E-value = 1.9e-505 ******************************************************************************** -------------------------------------------------------------------------------- Motif HDDTGTCGGCRRHDD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3321::::1:44333 pos.-specific C 2112::a::711311 probability G 122:a::a9:43233 matrix T 4447:9:::322233 bits 2.3 * ** 2.1 * ** 1.8 * *** 1.6 * *** Relative 1.4 ***** Entropy 1.1 ****** (12.4 bits) 0.9 ****** 0.7 ******* 0.5 ******* 0.2 ********* 0.0 --------------- Multilevel TTTTGTCGGCAAAAA consensus AAAC TGGCGT sequence C G TTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDTGTCGGCRRHDD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 738411 bayes= 9.39152 E= 1.9e-505 -3 18 -83 30 -1 -74 -6 39 -32 -59 10 47 -241 3 -521 130 -1847 -672 229 -1847 -417 -636 -211 166 -575 228 -562 -1007 -627 -1847 229 -1847 -170 -953 216 -1847 -475 170 -595 13 30 -95 83 -83 59 -99 56 -96 22 30 -24 -36 12 -72 46 -11 4 -51 36 -3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDTGTCGGCRRHDD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3637 E= 1.9e-505 0.291174 0.229860 0.114380 0.364586 0.294473 0.121529 0.195216 0.388782 0.237009 0.134726 0.217487 0.410778 0.055815 0.208139 0.005499 0.730547 0.000000 0.001925 0.998075 0.000000 0.016497 0.002475 0.047017 0.934012 0.005499 0.990102 0.004124 0.000275 0.003849 0.000000 0.996151 0.000000 0.091559 0.000275 0.908166 0.000000 0.010998 0.661809 0.003299 0.323893 0.365961 0.105032 0.362387 0.166621 0.445972 0.102282 0.299698 0.152048 0.345340 0.251031 0.172395 0.231235 0.321419 0.123178 0.280451 0.274952 0.304922 0.143250 0.260929 0.290899 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDTGTCGGCRRHDD MEME-1 regular expression -------------------------------------------------------------------------------- [TAC][TA][TAG][TC]GTCGG[CT][AG][AG][ACT][AGT][ATG] -------------------------------------------------------------------------------- Time 76.73 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTTYTTYTTYTTCTTYTTYT MEME-2 width = 21 sites = 868 llr = 9162 E-value = 2.8e-050 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTCTTYTTYT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1111:1:11::::1::::::1 pos.-specific C 25:242161242161242241 probability G 2111:1111:1:11:::1:12 matrix T 538766938757829867756 bits 2.3 2.1 1.8 1.6 Relative 1.4 Entropy 1.1 * (15.2 bits) 0.9 * * ** *** * 0.7 * * ******* ****** 0.5 ******************* 0.2 ********************* 0.0 --------------------- Multilevel TCTTTTTCTTTTTCTTTTTTT consensus T CC T CCC T CCCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTCTTYTTYT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 716559 bayes= 11.9844 E= 2.8e-050 -132 -43 -3 84 -103 121 -82 -14 -172 -646 -146 149 -245 6 -171 118 -800 98 -234 91 -242 -4 -62 105 -325 -201 -179 154 -239 152 -182 2 -169 -171 -153 139 -325 28 -388 125 -1641 94 -176 89 -1641 11 -266 134 -1641 -89 -124 144 -153 153 -104 -49 -442 -91 -1641 157 -800 -31 -214 141 -1641 99 -246 91 -1641 10 -63 113 -1641 19 -288 132 -800 104 -94 68 -165 -82 -23 106 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTCTTYTTYT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 868 E= 2.8e-050 0.118664 0.150922 0.199309 0.531106 0.145161 0.470046 0.115207 0.269585 0.089862 0.002304 0.073733 0.834101 0.054147 0.211982 0.062212 0.671659 0.001152 0.402074 0.040323 0.556452 0.055300 0.198157 0.132488 0.614055 0.031106 0.050691 0.058756 0.859447 0.056452 0.585253 0.057604 0.300691 0.092166 0.062212 0.070276 0.775346 0.031106 0.247696 0.013825 0.707373 0.000000 0.390553 0.059908 0.549539 0.000000 0.218894 0.032258 0.748848 0.000000 0.109447 0.086406 0.804147 0.102535 0.587558 0.099078 0.210829 0.013825 0.108295 0.000000 0.877880 0.001152 0.163594 0.046083 0.789171 0.000000 0.404378 0.036866 0.558756 0.000000 0.217742 0.131336 0.650922 0.000000 0.232719 0.027650 0.739631 0.001152 0.419355 0.105991 0.473502 0.094470 0.115207 0.173963 0.616359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTCTTYTTYT MEME-2 regular expression -------------------------------------------------------------------------------- T[CT]T[TC][TC]TT[CT]T[TC][TC][TC]T[CT]TT[TC][TC][TC][TC]T -------------------------------------------------------------------------------- Time 141.78 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************