******************************************************************************** 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/AT1G29280_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/AT1G29280_peak_sequences.fasta -dna -oc out/AT1G29280 -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= 5434 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= 1156589 N= 5434 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.325 C 0.175 G 0.175 T 0.325 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 MGTTGACTTTW MEME-1 width = 11 sites = 5168 llr = 45290 E-value = 7.5e-486 ******************************************************************************** -------------------------------------------------------------------------------- Motif MGTTGACTTTW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 21:::a::223 pos.-specific C 4:::::a3111 probability G 27::a::::12 matrix T 22aa:::7655 bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Relative 1.5 ***** Entropy 1.3 ****** (12.6 bits) 1.0 ****** 0.8 ******* 0.5 ******* 0.3 ********** 0.0 ----------- Multilevel CGTTGACTTTT consensus AT CAAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGTTGACTTTW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1102249 bayes= 9.79614 E= 7.5e-486 -57 134 -3 -92 -250 -1898 206 -56 -1898 -1898 -548 161 -872 -1898 -490 160 -1898 -1898 253 -1898 161 -1898 -822 -1898 -1898 253 -1898 -1898 -409 58 -467 113 -42 -90 -179 91 -42 -92 -50 73 -35 -45 -7 47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGTTGACTTTW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5168 E= 7.5e-486 0.220201 0.436533 0.169892 0.173375 0.057856 0.000000 0.720975 0.221169 0.000000 0.000000 0.003870 0.996130 0.000774 0.000000 0.005805 0.993421 0.000000 0.000000 1.000000 0.000000 0.999420 0.000000 0.000580 0.000000 0.000000 1.000000 0.000000 0.000000 0.019156 0.259481 0.006772 0.714590 0.244002 0.092686 0.049923 0.613390 0.243808 0.091525 0.122098 0.542570 0.257159 0.126548 0.164861 0.451432 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGTTGACTTTW MEME-1 regular expression -------------------------------------------------------------------------------- [CA][GT]TTGAC[TC][TA][TA][TA] -------------------------------------------------------------------------------- Time 125.07 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARRARAARAAGAARAARAR MEME-2 width = 21 sites = 1006 llr = 10750 E-value = 7.2e-052 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARRARAARAAGAARAARAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 376568486578387567584 pos.-specific C 211::::12:::111:11::1 probability G 52244:612521612432523 matrix T 1::1:1:::::1::::1:::1 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 (15.4 bits) 1.0 ** ** * * * 0.8 * **** ***** * ** 0.5 ******************** 0.3 ********************* 0.0 --------------------- Multilevel GAAAAAGAAAAAGAAAAAAAA consensus A GG A GG A GGG GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARRARAARAAGAARAARAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1047909 bayes= 12.2573 E= 7.2e-052 -27 -9 155 -241 110 -62 11 -1662 94 -29 16 -304 68 -192 103 -208 88 -1662 106 -319 135 -227 -1662 -133 31 -1662 172 -361 131 -94 -83 -1662 96 13 -9 -466 64 -1662 150 -1662 118 -274 43 -1662 130 -412 -95 -176 -14 -89 182 -1662 127 -72 -105 -397 108 -125 21 -323 72 -354 137 -1662 90 -151 66 -258 110 -120 17 -341 60 -336 144 -419 122 -1662 32 -397 40 -72 93 -130 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARRARAARAAGAARAARAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1006 E= 7.2e-052 0.271372 0.162028 0.504970 0.061630 0.700795 0.112326 0.186879 0.000000 0.625249 0.141153 0.193837 0.039761 0.522863 0.045726 0.353877 0.077535 0.603380 0.000000 0.360835 0.035785 0.833996 0.035785 0.000000 0.130219 0.404573 0.000000 0.568588 0.026839 0.812127 0.090457 0.097416 0.000000 0.635189 0.188867 0.163022 0.012922 0.510934 0.000000 0.489066 0.000000 0.741551 0.025845 0.232604 0.000000 0.804175 0.009940 0.089463 0.096421 0.296223 0.093439 0.610338 0.000000 0.790258 0.105368 0.083499 0.020875 0.691849 0.072565 0.200795 0.034791 0.538767 0.014911 0.446322 0.000000 0.611332 0.060636 0.273360 0.054672 0.698807 0.075547 0.194831 0.030815 0.495030 0.016899 0.470179 0.017893 0.763419 0.000000 0.215706 0.020875 0.432406 0.105368 0.329026 0.133201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARRARAARAAGAARAARAR MEME-2 regular expression -------------------------------------------------------------------------------- [GA]AA[AG][AG]A[GA]AA[AG][AG]A[GA]A[AG][AG][AG]A[AG][AG][AG] -------------------------------------------------------------------------------- Time 236.14 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************