******************************************************************************** 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/AT1G76420_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/AT1G76420_peak_sequences.fasta -dna -oc out/AT1G76420 -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= 2787 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= 447702 N= 2787 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.321 C 0.179 G 0.179 T 0.321 Background letter frequencies (from file dataset with add-one prior applied): A 0.322 C 0.178 G 0.178 T 0.322 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TDRCGTGWDDWACAAGHA MEME-1 width = 18 sites = 1781 llr = 16237 E-value = 6.7e-340 ******************************************************************************** -------------------------------------------------------------------------------- Motif TDRCGTGWDDWACAAGHA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2341::334345197:26 pos.-specific C ::19:::112215:3:32 probability G :24:7:7133222::91: matrix T 841:3a:522322:::32 bits 2.5 2.2 2.0 * * 1.7 * * Relative 1.5 *** * Entropy 1.2 **** * * (13.2 bits) 1.0 * **** * * 0.7 * **** *** 0.5 * **** **** 0.2 ******* ***** * 0.0 ------------------ Multilevel TTACGTGTAAAACAAGTA consensus AG T AAGGTTG C CT sequence G T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TDRCGTGWDDWACAAGHA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 400323 bayes= 9.76806 E= 6.7e-340 -102 -485 -1744 138 3 -314 35 40 36 -77 105 -152 -208 235 -1744 -426 -1744 -1744 202 -20 -1744 -599 -1744 163 -8 -461 195 -816 -28 -38 -94 65 30 -41 59 -68 10 -14 74 -71 24 5 -5 -29 68 -122 -5 -45 -170 146 46 -96 156 -292 -731 -349 111 64 -264 -1744 -346 -1744 240 -336 -40 77 -35 -3 87 -24 -272 -47 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TDRCGTGWDDWACAAGHA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 1781 E= 6.7e-340 0.158338 0.006176 0.000000 0.835486 0.327906 0.020213 0.226839 0.425042 0.413812 0.104436 0.369455 0.112296 0.076362 0.906794 0.000000 0.016844 0.000000 0.000000 0.719259 0.280741 0.000000 0.002807 0.000000 0.997193 0.304885 0.007299 0.686693 0.001123 0.265581 0.136440 0.092645 0.505334 0.396968 0.134194 0.268389 0.200449 0.344750 0.161145 0.297586 0.196519 0.380124 0.184166 0.171814 0.263897 0.516002 0.076362 0.171252 0.236384 0.099382 0.490736 0.244806 0.165076 0.946659 0.023582 0.001123 0.028636 0.693992 0.277372 0.028636 0.000000 0.029197 0.000000 0.939360 0.031443 0.243683 0.302639 0.139248 0.314430 0.588995 0.151039 0.026951 0.233015 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TDRCGTGWDDWACAAGHA MEME-1 regular expression -------------------------------------------------------------------------------- T[TAG][AG]C[GT]T[GA][TA][AGT][AG][AT][AT][CG]A[AC]G[TCA][AT] -------------------------------------------------------------------------------- Time 126.83 secs. ******************************************************************************** ******************************************************************************** MOTIF GTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACGCGCTACCATTG MEME-2 width = 50 sites = 12 llr = 704 E-value = 1.2e-035 ******************************************************************************** -------------------------------------------------------------------------------- Motif GTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACGCGCTACCATTG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::8a:::aa:a:::a8:::3:::8::::38:3:8:8::3:::8::8::: pos.-specific C :3:3::8:::8:a:a::aa::8::3:a3:::3:8::3a383a::a8:::: probability G a:8::33a::3::a::3::::33a::::a838::2a::8:8::3::3:3a matrix T :83::8:::::::::::::a8:8::a:8::::83::::::::a::3:a8: bits 2.5 * * *** ** * * * * * * * * 2.2 * * *** ** * * * * * * * * 2.0 * * *** ** * * * * * * * * 1.7 * * ********** *** * * ** * * * ** *** * * * Relative 1.5 * * * ********** *** * * ** ** * * * ****** ** * * Entropy 1.2 * * * ********** *** * * ** ** * *** ****** ** * * (84.7 bits) 1.0 ******************** *********** ***************** 0.7 ************************************************** 0.5 ************************************************** 0.2 ************************************************** 0.0 -------------------------------------------------- Multilevel GTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACGCGCTACCATTG consensus CTC GG G G AGG C C AGCAT C CAC G TG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACGCGCTACCATTG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 311139 bayes= 16.2472 E= 1.2e-035 -1023 -1023 249 -1023 -1023 49 -1023 122 -1023 -1023 207 -37 122 49 -1023 -1023 163 -1023 -1023 -1023 -1023 -1023 49 122 -1023 207 49 -1023 -1023 -1023 249 -1023 163 -1023 -1023 -1023 163 -1023 -1023 -1023 -1023 207 49 -1023 163 -1023 -1023 -1023 -1023 249 -1023 -1023 -1023 -1023 249 -1023 -1023 249 -1023 -1023 163 -1023 -1023 -1023 122 -1023 49 -1023 -1023 249 -1023 -1023 -1023 249 -1023 -1023 -1023 -1023 -1023 163 -37 -1023 -1023 122 -1023 207 49 -1023 -1023 -1023 49 122 -1023 -1023 249 -1023 122 49 -1023 -1023 -1023 -1023 -1023 163 -1023 249 -1023 -1023 -1023 49 -1023 122 -1023 -1023 249 -1023 -37 -1023 207 -1023 122 -1023 49 -1023 -1023 49 207 -1023 -37 -1023 -1023 122 -1023 207 -1023 -37 137 -1023 -9 -1023 -1023 -1023 249 -1023 122 49 -1023 -1023 -1023 249 -1023 -1023 -1023 49 207 -1023 -37 207 -1023 -1023 -1023 49 207 -1023 -1023 249 -1023 -1023 -1023 -1023 -1023 163 122 -1023 49 -1023 -1023 249 -1023 -1023 -1023 207 -1023 -37 122 -1023 49 -1023 -1023 -1023 -1023 163 -1023 -1023 49 122 -1023 -1023 249 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACGCGCTACCATTG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 12 E= 1.2e-035 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 0.750000 0.250000 0.750000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.750000 0.000000 0.750000 0.000000 0.250000 0.833333 0.000000 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.000000 0.250000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.250000 0.750000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GTGAATCGAACACGCAACCTTCTGATCTGGAGTCAGACGCGCTACCATTG MEME-2 regular expression -------------------------------------------------------------------------------- G[TC][GT][AC]A[TG][CG]GAA[CG]ACGCA[AG]CCT[TA][CG][TG]G[AC]TC[TC]G[GA][AG][GC][TA][CT]AG[AC]C[GC][CA][GC]CT[AG]C[CT][AG]T[TG]G -------------------------------------------------------------------------------- Time 237.45 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************