******************************************************************************** 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/AT5G39760_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/AT5G39760_peak_sequences.fasta -dna -oc out/AT5G39760 -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= 6656 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= 1870918 N= 6656 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.385 C 0.115 G 0.115 T 0.385 Background letter frequencies (from file dataset with add-one prior applied): A 0.385 C 0.115 G 0.115 T 0.385 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HCCGCGGTRTACCGCGGGTTAWAAYCTA MEME-1 width = 28 sites = 26 llr = 902 E-value = 1.6e-024 ******************************************************************************** -------------------------------------------------------------------------------- Motif HCCGCGGTRTACCGCGGGTTAWAAYCTA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3::::2::51a::::1:2::a6681::a pos.-specific C 59a:9::3:::7a:a:::::::2:3a:: probability G :::9:8a:5::3:a:9a8:3:::::::: matrix T 21::1::7:9::::::::a7:4216:a: bits 3.1 * * 2.8 * * *** * * 2.5 **** * ***** * 2.2 ****** ****** * Relative 1.9 ****** ******* * Entropy 1.6 ****** ******* * (50.0 bits) 1.2 ****** ********* * *** 0.9 ******************** *** 0.6 ********************* ***** 0.3 **************************** 0.0 ---------------------------- Multilevel CCCGCGGTATACCGCGGGTTAAAATCTA consensus A CG G G T C sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCCGCGGTRTACCGCGGGTTAWAAYCTA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 1691205 bayes= 17.1536 E= 1.6e-024 -32 201 -1134 -74 -1134 301 -1134 -232 -1134 307 -1134 -332 -332 -158 301 -1134 -1134 301 -1134 -232 -100 -1134 282 -1134 -332 -1134 307 -1134 -1134 123 -1134 92 38 -1134 201 -332 -232 -1134 -1134 126 138 -1134 -1134 -1134 -332 259 123 -1134 -1134 307 -1134 -332 -332 -1134 307 -1134 -1134 312 -1134 -1134 -174 -1134 295 -1134 -332 -1134 307 -1134 -132 -1134 288 -1134 -1134 -1134 -1134 138 -1134 -158 142 76 132 -158 -1134 -1134 68 -1134 -1134 0 68 75 -1134 -100 113 -158 -1134 -174 -232 159 -1134 58 -1134 312 -1134 -1134 -1134 -1134 -1134 138 132 -1134 -1134 -332 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCCGCGGTRTACCGCGGGTTAWAAYCTA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 26 E= 1.6e-024 0.307692 0.461538 0.000000 0.230769 0.000000 0.923077 0.000000 0.076923 0.000000 0.961538 0.000000 0.038462 0.038462 0.038462 0.923077 0.000000 0.000000 0.923077 0.000000 0.076923 0.192308 0.000000 0.807692 0.000000 0.038462 0.000000 0.961538 0.000000 0.000000 0.269231 0.000000 0.730769 0.500000 0.000000 0.461538 0.038462 0.076923 0.000000 0.000000 0.923077 1.000000 0.000000 0.000000 0.000000 0.038462 0.692308 0.269231 0.000000 0.000000 0.961538 0.000000 0.038462 0.038462 0.000000 0.961538 0.000000 0.000000 1.000000 0.000000 0.000000 0.115385 0.000000 0.884615 0.000000 0.038462 0.000000 0.961538 0.000000 0.153846 0.000000 0.846154 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.038462 0.307692 0.653846 0.961538 0.038462 0.000000 0.000000 0.615385 0.000000 0.000000 0.384615 0.615385 0.192308 0.000000 0.192308 0.846154 0.038462 0.000000 0.115385 0.076923 0.346154 0.000000 0.576923 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.961538 0.000000 0.000000 0.038462 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HCCGCGGTRTACCGCGGGTTAWAAYCTA MEME-1 regular expression -------------------------------------------------------------------------------- [CAT]CCGCGG[TC][AG]TA[CG]CGCGGGT[TG]A[AT]AA[TC]CTA -------------------------------------------------------------------------------- Time 68.95 secs. ******************************************************************************** ******************************************************************************** MOTIF CCTSCCAAACCCGTCCCGCCAAMYCVKYC MEME-2 width = 29 sites = 37 llr = 1162 E-value = 1.5e-021 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCTSCCAAACCCGTCCCGCCAAMYCVKYC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21212299a::::::1:2::985:22::: pos.-specific C 86136811:989:1878:99:1447425a probability G :1:5::::::::a::::6:::::::44:: matrix T :2812::::111:922221:12151145: bits 3.1 * 2.8 * * 2.5 * ** ** * 2.2 * **** * ** * Relative 1.9 * * **** * * ** * Entropy 1.6 * * **** *** ** * * (45.3 bits) 1.2 ** *** ********* ** * ** 0.9 ** ****************** ****** 0.6 ***************************** 0.3 ***************************** 0.0 ----------------------------- Multilevel CCTGCCAAACCCGTCCCGCCAAATCCGCC consensus C T T CC GTT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTSCCAAACCCGTCCCGCCAAMYCVKYC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 1684549 bayes= 16.3476 E= 1.5e-021 -103 277 -1185 -383 -225 250 -50 -103 -103 -108 -1185 97 -225 150 200 -151 -125 250 -1185 -103 -125 287 -1185 -1185 130 -108 -1185 -1185 125 -108 -208 -1185 134 -1185 -208 -1185 -383 300 -1185 -283 -383 287 -1185 -151 -1185 300 -1185 -225 -383 -1185 308 -1185 -1185 -108 -1185 130 -383 277 -208 -125 -225 261 -1185 -83 -1185 287 -1185 -125 -103 -1185 231 -66 -383 300 -1185 -283 -383 300 -208 -383 130 -1185 -1185 -283 97 -108 -1185 -103 41 182 -1185 -225 -383 191 -1185 49 -125 267 -1185 -183 -103 172 172 -283 -1185 72 191 -3 -1185 216 -1185 34 -1185 312 -1185 -1185 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTSCCAAACCCGTCCCGCCAAMYCVKYC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 37 E= 1.5e-021 0.189189 0.783784 0.000000 0.027027 0.081081 0.648649 0.081081 0.189189 0.189189 0.054054 0.000000 0.756757 0.081081 0.324324 0.459459 0.135135 0.162162 0.648649 0.000000 0.189189 0.162162 0.837838 0.000000 0.000000 0.945946 0.054054 0.000000 0.000000 0.918919 0.054054 0.027027 0.000000 0.972973 0.000000 0.027027 0.000000 0.027027 0.918919 0.000000 0.054054 0.027027 0.837838 0.000000 0.135135 0.000000 0.918919 0.000000 0.081081 0.027027 0.000000 0.972973 0.000000 0.000000 0.054054 0.000000 0.945946 0.027027 0.783784 0.027027 0.162162 0.081081 0.702703 0.000000 0.216216 0.000000 0.837838 0.000000 0.162162 0.189189 0.000000 0.567568 0.243243 0.027027 0.918919 0.000000 0.054054 0.027027 0.918919 0.027027 0.027027 0.945946 0.000000 0.000000 0.054054 0.756757 0.054054 0.000000 0.189189 0.513514 0.405405 0.000000 0.081081 0.027027 0.432432 0.000000 0.540541 0.162162 0.729730 0.000000 0.108108 0.189189 0.378378 0.378378 0.054054 0.000000 0.189189 0.432432 0.378378 0.000000 0.513514 0.000000 0.486486 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCTSCCAAACCCGTCCCGCCAAMYCVKYC MEME-2 regular expression -------------------------------------------------------------------------------- CCT[GC]CCAAACCCGTC[CT]C[GT]CCAA[AC][TC]C[CG][GT][CT]C -------------------------------------------------------------------------------- Time 149.95 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************