******************************************************************************** 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/AT4G23550_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/AT4G23550_peak_sequences.fasta -dna -oc out/AT4G23550 -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= 6965 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= 1644126 N= 6965 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.335 C 0.165 G 0.165 T 0.335 Background letter frequencies (from file dataset with add-one prior applied): A 0.336 C 0.164 G 0.164 T 0.336 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAAGTCAAMD MEME-1 width = 11 sites = 6949 llr = 59327 E-value = 8.1e-421 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5678:::aa32 pos.-specific C 21::::a::62 probability G 1112a:::::3 matrix T 222::a:::13 bits 2.6 * * 2.4 * * 2.1 * * 1.8 * * Relative 1.6 ***** Entropy 1.3 ***** (12.3 bits) 1.0 ***** 0.8 ******* 0.5 ******** 0.3 ********** 0.0 ----------- Multilevel AAAAGTCAACG consensus T T AT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1574476 bayes= 10.1181 E= 8.1e-421 54 -1 -33 -61 87 -76 -85 -77 108 -344 -132 -68 123 -1941 16 -354 -861 -1941 261 -694 -887 -1941 -1941 157 -694 261 -1941 -960 156 -483 -915 -610 154 -1941 -311 -960 0 181 -402 -211 -70 -7 105 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6949 E= 8.1e-421 0.487696 0.162326 0.130235 0.219744 0.615484 0.096561 0.090661 0.197295 0.709455 0.015110 0.065621 0.209814 0.788027 0.000000 0.183048 0.028925 0.000863 0.000000 0.996402 0.002734 0.000720 0.000000 0.000000 0.999280 0.002734 0.996834 0.000000 0.000432 0.989063 0.005756 0.000288 0.004893 0.980573 0.000000 0.018996 0.000432 0.337027 0.574903 0.010073 0.077997 0.207080 0.155562 0.337890 0.299468 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 regular expression -------------------------------------------------------------------------------- [AT]A[AT]AGTCAA[CA][GTA] -------------------------------------------------------------------------------- Time 79.86 secs. ******************************************************************************** ******************************************************************************** MOTIF RAAAAARAARAARAAAAAAAR MEME-2 width = 21 sites = 1400 llr = 15001 E-value = 1.8e-046 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAAAARAARAARAAAAAAAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 66677959666a597667684 pos.-specific C :22111::::1:1:::211:2 probability G 42232:41342:5133323:2 matrix T 111::::11:1::::1:1:12 bits 2.6 2.4 2.1 1.8 Relative 1.6 * Entropy 1.3 * (15.5 bits) 1.0 * * * ** 0.8 * ***** * **** ** 0.5 * ***************** 0.3 ******************** 0.0 --------------------- Multilevel AAAAAAAAAAAAGAAAAAAAA consensus GG G G GGG A GGG G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAARAARAARAAAAAAAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1504826 bayes= 12.359 E= 1.8e-046 79 -1710 113 -252 73 -10 46 -239 78 11 9 -221 99 -171 78 -1710 111 -74 6 -656 145 -161 -1710 -356 65 -186 138 -1710 138 -1710 -150 -240 92 -217 66 -234 82 -1710 115 -295 94 -81 34 -265 157 -1710 -1710 -788 42 -152 159 -1710 142 -1710 -150 -305 107 -1710 85 -1710 89 -367 86 -232 75 -6 76 -1710 97 -72 1 -215 91 -113 84 -1710 131 -201 -1710 -140 22 15 59 -91 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAARAARAARAAAAAAAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1400 E= 1.8e-046 0.582143 0.000000 0.359286 0.058571 0.558571 0.152143 0.225000 0.064286 0.576429 0.176429 0.174286 0.072857 0.669286 0.050000 0.280714 0.000000 0.728571 0.097857 0.170000 0.003571 0.917857 0.053571 0.000000 0.028571 0.527857 0.045000 0.427143 0.000000 0.878571 0.000000 0.057857 0.063571 0.638571 0.036429 0.258571 0.066429 0.593571 0.000000 0.362857 0.043571 0.645714 0.093571 0.207143 0.053571 0.998571 0.000000 0.000000 0.001429 0.450714 0.057143 0.492143 0.000000 0.901429 0.000000 0.057857 0.040714 0.705714 0.000000 0.294286 0.000000 0.623571 0.012857 0.296429 0.067143 0.566429 0.157143 0.276429 0.000000 0.660714 0.099286 0.164286 0.075714 0.631429 0.075000 0.293571 0.000000 0.831429 0.040714 0.000000 0.127857 0.392857 0.182143 0.246429 0.178571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAAAARAARAARAAAAAAAR MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG]A[AG]AA[AG]A[AG][AG][AG]A[GA]A[AG][AG][AG]A[AG]A[AG] -------------------------------------------------------------------------------- Time 152.98 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************