******************************************************************************** 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/AT5G25810_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/AT5G25810_peak_sequences.fasta -dna -oc out/AT5G25810 -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= 6780 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= 1502349 N= 6780 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.291 C 0.209 G 0.209 T 0.291 Background letter frequencies (from file dataset with add-one prior applied): A 0.293 C 0.207 G 0.207 T 0.293 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YGTCGGYGDND MEME-1 width = 11 sites = 6720 llr = 57101 E-value = 6.4e-480 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGTCGGYGDND MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1::::::2333 pos.-specific C 3::a::41131 probability G :a1:aa:5323 matrix T 6:9:::62233 bits 2.3 * *** 2.0 * *** 1.8 * *** 1.6 * *** Relative 1.4 * *** Entropy 1.1 ***** (12.3 bits) 0.9 ****** 0.7 ****** 0.5 ******* 0.2 ******** 0.0 ----------- Multilevel TGTCGGTGAAG consensus C C GTT sequence TCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTCGGYGDND MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1434549 bayes= 9.85367 E= 6.4e-480 -186 72 -320 92 -1936 -1936 227 -1936 -286 -1936 -115 157 -1936 227 -1936 -1936 -1936 -1936 227 -1936 -1936 -1936 227 -1936 -836 93 -1936 104 -62 -103 130 -55 24 -73 66 -54 5 31 -45 -2 -10 -72 65 -8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTCGGYGDND MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6720 E= 6.4e-480 0.080506 0.341369 0.022619 0.555506 0.000000 0.000000 1.000000 0.000000 0.040179 0.000000 0.093601 0.866220 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000893 0.395387 0.000000 0.603720 0.190179 0.101488 0.508929 0.199405 0.346429 0.124554 0.327530 0.201488 0.302679 0.257143 0.152232 0.287946 0.272768 0.125893 0.325298 0.276042 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGTCGGYGDND MEME-1 regular expression -------------------------------------------------------------------------------- [TC]GTCGG[TC]G[AGT][ATC][GTA] -------------------------------------------------------------------------------- Time 71.62 secs. ******************************************************************************** ******************************************************************************** MOTIF YCDYCDYCKYCTYCKYCDYCG MEME-2 width = 21 sites = 1775 llr = 19008 E-value = 1.4e-115 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCDYCDYCKYCTYCKYCDYCG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1131:2:121:2::2::3:12 pos.-specific C 47:68167:57158:69:562 probability G 113::2::31:2::3::31:4 matrix T 415424415436415414322 bits 2.3 2.0 1.8 * 1.6 * Relative 1.4 * * * * Entropy 1.1 * * * ** (15.4 bits) 0.9 * ** * ** ** 0.7 * ** ** * ** ** ** 0.5 ***** ***** ***** ** 0.2 ***** *************** 0.0 --------------------- Multilevel CCTCCTCCTCCTCCTCCTCCG consensus T ATTGT GTTGT GT GTTA sequence G A A A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCDYCDYCKYCTYCKYCDYCG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1366749 bayes= 11.9038 E= 1.4e-115 -182 99 -110 48 -126 173 -188 -113 -16 -1744 30 72 -214 142 -1744 38 -1744 187 -1744 -27 -38 -82 16 54 -329 142 -1744 50 -155 184 -224 -133 -47 -1744 62 68 -231 125 -150 36 -1744 182 -1744 -11 -82 -200 7 95 -1744 131 -224 60 -291 203 -1744 -136 -54 -1744 37 86 -1744 154 -1744 44 -743 215 -377 -218 -10 -262 58 38 -438 138 -76 14 -197 161 -228 -23 -54 -11 102 -64 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCDYCDYCKYCTYCKYCDYCG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1775 E= 1.4e-115 0.082817 0.411831 0.096901 0.408451 0.122254 0.687887 0.056338 0.133521 0.261972 0.000000 0.254648 0.483380 0.066479 0.553239 0.000000 0.380282 0.000000 0.757183 0.000000 0.242817 0.224225 0.117183 0.231549 0.427042 0.029859 0.555493 0.000000 0.414648 0.099718 0.739718 0.043944 0.116620 0.211831 0.000000 0.317746 0.470423 0.059155 0.491831 0.073239 0.375775 0.000000 0.729577 0.000000 0.270423 0.165634 0.051831 0.217465 0.565070 0.000000 0.512676 0.043944 0.443380 0.038873 0.847324 0.000000 0.113803 0.201690 0.000000 0.267042 0.531268 0.000000 0.602817 0.000000 0.397183 0.001690 0.918310 0.015211 0.064789 0.273803 0.033803 0.310423 0.381972 0.014085 0.539718 0.122817 0.323380 0.074930 0.632676 0.042817 0.249577 0.201127 0.191549 0.419718 0.187606 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCDYCDYCKYCTYCKYCDYCG MEME-2 regular expression -------------------------------------------------------------------------------- [CT]C[TAG][CT][CT][TGA][CT]C[TGA][CT][CT][TG][CT]C[TGA][CT]C[TGA][CT][CT][GA] -------------------------------------------------------------------------------- Time 136.58 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************