******************************************************************************** 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/AT4G14770_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/AT4G14770_peak_sequences.fasta -dna -oc out/AT4G14770 -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= 1941 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= 439929 N= 1941 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.396 C 0.104 G 0.104 T 0.396 Background letter frequencies (from file dataset with add-one prior applied): A 0.397 C 0.103 G 0.103 T 0.397 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTCATGTATTGAAYARTTTATATTCGTTTTTAAAAATTCAAATTATR MEME-1 width = 47 sites = 61 llr = 2264 E-value = 5.4e-105 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTCATGTATTGAAYARTTTATATTCGTTTTTAAAAATTCAAATTATR MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::8:138::1871a5:3:9:7:::21:::19aaa7:::7aa::9:3 pos.-specific C ::7:22:::::::6::::1::::29:::::::::::::7::::3:2: probability G :::2:6:1::82:::5:::::3:::8:::::::::::::3:::::16 matrix T aa3:8261aa1:33::a79:91a81:9aaa91:::3aa3:::97:71 bits 3.3 2.9 2.6 * 2.3 * * Relative 2.0 * * ** Entropy 1.6 * * ** * (53.5 bits) 1.3 *** * * * *** * ** *** *** *** * * 1.0 ****** **** **** *** ******** **** ******* * * 0.7 ****** ***** **** ***************************** 0.3 *********************************************** 0.0 ----------------------------------------------- Multilevel TTCATGTATTGAACAGTTTATATTCGTTTTTAAAAATTCAAATTATG consensus T C A TT A A G T TG C A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCATGTATTGAAYARTTTATATTCGTTTTTAAAAATTCAAATTATR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 47 n= 350643 bayes= 13.7757 E= 5.4e-105 -1257 -1257 -1257 133 -1257 -1257 -266 131 -1257 280 -1257 -51 102 -1257 93 -1257 -1257 104 -1257 99 -260 80 251 -127 -43 -266 -107 69 105 -266 -66 -201 -1257 -266 -1257 131 -459 -266 -1257 129 -201 -1257 302 -260 102 -1257 93 -1257 83 -1257 -166 -60 -201 243 -1257 -20 133 -1257 -1257 -1257 26 -1257 234 -1257 -459 -1257 -1257 131 -35 -1257 -1257 80 -1257 -7 -1257 118 124 -1257 -107 -459 -301 -266 -1257 124 73 -1257 143 -260 -1257 -1257 -1257 133 -1257 93 -1257 102 -1257 307 -1257 -160 -114 -1257 296 -459 -201 -1257 -1257 118 -1257 -1257 -1257 133 -1257 -1257 -1257 133 -459 -1257 -1257 131 -179 -266 -1257 113 121 -1257 -1257 -227 131 -1257 -266 -1257 133 -1257 -1257 -1257 131 -1257 -1257 -459 90 -1257 -1257 -60 -1257 -1257 -1257 133 -1257 -266 -1257 131 -359 266 -1257 -35 86 -1257 143 -1257 133 -1257 -1257 -1257 129 -1257 -1257 -359 -459 -107 -1257 124 -301 151 -1257 73 121 -1257 -107 -359 -1257 93 -66 90 -20 -1257 251 -260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCATGTATTGAAYARTTTATATTCGTTTTTAAAAATTCAAATTATR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 47 nsites= 61 E= 5.4e-105 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.016393 0.983607 0.000000 0.721311 0.000000 0.278689 0.803279 0.000000 0.196721 0.000000 0.000000 0.213115 0.000000 0.786885 0.065574 0.180328 0.590164 0.163934 0.295082 0.016393 0.049180 0.639344 0.819672 0.016393 0.065574 0.098361 0.000000 0.016393 0.000000 0.983607 0.016393 0.016393 0.000000 0.967213 0.098361 0.000000 0.836066 0.065574 0.803279 0.000000 0.196721 0.000000 0.704918 0.000000 0.032787 0.262295 0.098361 0.557377 0.000000 0.344262 1.000000 0.000000 0.000000 0.000000 0.475410 0.000000 0.524590 0.000000 0.016393 0.000000 0.000000 0.983607 0.311475 0.000000 0.000000 0.688525 0.000000 0.098361 0.000000 0.901639 0.934426 0.000000 0.049180 0.016393 0.049180 0.016393 0.000000 0.934426 0.655738 0.000000 0.278689 0.065574 0.000000 0.000000 0.000000 1.000000 0.000000 0.196721 0.000000 0.803279 0.000000 0.868852 0.000000 0.131148 0.180328 0.000000 0.803279 0.016393 0.098361 0.000000 0.000000 0.901639 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.016393 0.000000 0.000000 0.983607 0.114754 0.016393 0.000000 0.868852 0.918033 0.000000 0.000000 0.081967 0.983607 0.000000 0.016393 0.000000 1.000000 0.000000 0.000000 0.000000 0.983607 0.000000 0.000000 0.016393 0.737705 0.000000 0.000000 0.262295 0.000000 0.000000 0.000000 1.000000 0.000000 0.016393 0.000000 0.983607 0.032787 0.655738 0.000000 0.311475 0.721311 0.000000 0.278689 0.000000 1.000000 0.000000 0.000000 0.000000 0.967213 0.000000 0.000000 0.032787 0.016393 0.049180 0.000000 0.934426 0.049180 0.295082 0.000000 0.655738 0.918033 0.000000 0.049180 0.032787 0.000000 0.196721 0.065574 0.737705 0.344262 0.000000 0.590164 0.065574 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTCATGTATTGAAYARTTTATATTCGTTTTTAAAAATTCAAATTATR MEME-1 regular expression -------------------------------------------------------------------------------- TT[CT]A[TC]G[TA]ATTGA[AT][CT]A[GA]T[TA]TAT[AG]TTCGTTTTTAAAA[AT]TT[CT][AG]AAT[TC]AT[GA] -------------------------------------------------------------------------------- Time 72.47 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT MEME-2 width = 36 sites = 2 llr = 93 E-value = 2.2e-081 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::aaaaa:a:aa::a:a:aaa:a::a:aa:: pos.-specific C :::aa:a:::::::::::a::::::::::::::::: probability G :::::a::::::::a:::::::::::a::a:a::a: matrix T aaa:::::::::a::::a::a:a:::::a::::::a bits 3.3 **** * * * * * * 2.9 **** * * * * * * 2.6 **** * * * * * * 2.3 **** * * * * * * Relative 2.0 **** * * * * * * Entropy 1.6 **** * * * * * * (67.4 bits) 1.3 ************************************ 1.0 ************************************ 0.7 ************************************ 0.3 ************************************ 0.0 ------------------------------------ Multilevel TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 36 n= 371994 bayes= 15.7394 E= 2.2e-081 -765 -765 -765 133 -765 -765 -765 133 -765 -765 -765 133 -765 327 -765 -765 -765 327 -765 -765 -765 -765 327 -765 -765 327 -765 -765 133 -765 -765 -765 133 -765 -765 -765 133 -765 -765 -765 133 -765 -765 -765 133 -765 -765 -765 -765 -765 -765 133 133 -765 -765 -765 -765 -765 327 -765 133 -765 -765 -765 133 -765 -765 -765 -765 -765 -765 133 -765 327 -765 -765 133 -765 -765 -765 -765 -765 -765 133 133 -765 -765 -765 -765 -765 -765 133 133 -765 -765 -765 133 -765 -765 -765 133 -765 -765 -765 -765 -765 327 -765 133 -765 -765 -765 -765 -765 -765 133 -765 -765 327 -765 133 -765 -765 -765 -765 -765 327 -765 133 -765 -765 -765 133 -765 -765 -765 -765 -765 327 -765 -765 -765 -765 133 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 36 nsites= 2 E= 2.2e-081 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 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 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 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 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT MEME-2 regular expression -------------------------------------------------------------------------------- TTTCCGCAAAAATAGAATCATATAAAGATGAGAAGT -------------------------------------------------------------------------------- Time 145.22 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************