******************************************************************************** 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/AT1G76880_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/AT1G76880_peak_sequences.fasta -dna -oc out/AT1G76880 -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= 3419 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= 924468 N= 3419 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.371 C 0.129 G 0.129 T 0.371 Background letter frequencies (from file dataset with add-one prior applied): A 0.372 C 0.128 G 0.128 T 0.372 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TWTTTTTTTACYKTT MEME-1 width = 15 sites = 3394 llr = 23871 E-value = 1.2e-141 ******************************************************************************** -------------------------------------------------------------------------------- Motif TWTTTTTTTACYKTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 232322::19:1212 pos.-specific C 1121::::1:95111 probability G 1111::::::::211 matrix T 655688aa9114476 bits 3.0 2.7 * 2.4 * 2.1 * Relative 1.8 * Entropy 1.5 ** * (10.1 bits) 1.2 ** * 0.9 ******* 0.6 ******** 0.3 ********** 0.0 --------------- Multilevel TTTTTTTTTACCTTT consensus AAAAA TG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWTTTTTTTACYKTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 876602 bayes= 9.81218 E= 1.2e-141 -84 14 -38 57 -39 -17 -39 44 -67 39 -101 52 -46 -66 -45 58 -78 -296 -386 103 -130 -1837 -776 119 -1837 -437 -518 141 -1837 -1837 -1837 143 -246 -123 -390 122 127 -239 -1837 -230 -1837 288 -506 -282 -220 189 -279 19 -117 14 96 26 -151 21 -87 81 -95 10 -17 58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWTTTTTTTACYKTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3394 E= 1.2e-141 0.207130 0.141131 0.098114 0.553624 0.284031 0.113730 0.097525 0.504714 0.234532 0.167354 0.063642 0.534473 0.270772 0.081025 0.093695 0.554508 0.216264 0.016500 0.008839 0.758397 0.151149 0.000000 0.000589 0.848262 0.000000 0.006187 0.003536 0.990277 0.000000 0.000000 0.000000 1.000000 0.067767 0.054508 0.008544 0.869181 0.899823 0.024455 0.000000 0.075722 0.000000 0.943430 0.003830 0.052740 0.080731 0.475250 0.018562 0.425457 0.165292 0.141131 0.249558 0.444019 0.130524 0.147613 0.070124 0.651738 0.192398 0.137006 0.113435 0.557160 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWTTTTTTTACYKTT MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TA][TA][TA][TA]TTTTAC[CT][TG]TT -------------------------------------------------------------------------------- Time 120.96 secs. ******************************************************************************** ******************************************************************************** MOTIF CCGCGGTATACCGCGGGTTAAAATCTAGT MEME-2 width = 29 sites = 17 llr = 708 E-value = 1.2e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCGCGGTATACCGCGGGTTAAAATCTAGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::::12:9:a::::1::::aaaa:::91: pos.-specific C 9a:a::::::9a:a:::1::::::a:::: probability G ::a:98:1::::a:9aa::::::::::9: matrix T 1:::::a:a:1::::::9a::::a:a1:a bits 3.0 *** *** ** * 2.7 **** ****** * * 2.4 ***** ******* * * 2.1 ****** ******* * * Relative 1.8 ****** ******* * * Entropy 1.5 ******* ********* ******** ** (60.1 bits) 1.2 ***************************** 0.9 ***************************** 0.6 ***************************** 0.3 ***************************** 0.0 ----------------------------- Multilevel CCGCGGTATACCGCGGGTTAAAATCTAGT consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCGGTATACCGCGGGTTAAAATCTAGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 828736 bayes= 16.9381 E= 1.2e-007 -1073 288 -1073 -266 -1073 297 -1073 -1073 -1073 -1073 297 -1073 -1073 297 -1073 -1073 -166 -1073 278 -1073 -107 -1073 268 -1073 -1073 -1073 -1073 143 134 -1073 -112 -1073 -1073 -1073 -1073 143 143 -1073 -1073 -1073 -1073 278 -1073 -166 -1073 297 -1073 -1073 -1073 -1073 297 -1073 -1073 297 -1073 -1073 -266 -1073 288 -1073 -1073 -1073 297 -1073 -1073 -1073 297 -1073 -1073 -112 -1073 134 -1073 -1073 -1073 143 143 -1073 -1073 -1073 143 -1073 -1073 -1073 143 -1073 -1073 -1073 143 -1073 -1073 -1073 -1073 -1073 -1073 143 -1073 297 -1073 -1073 -1073 -1073 -1073 143 134 -1073 -1073 -266 -266 -1073 288 -1073 -1073 -1073 -1073 143 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCGGTATACCGCGGGTTAAAATCTAGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 17 E= 1.2e-007 0.000000 0.941176 0.000000 0.058824 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.117647 0.000000 0.882353 0.000000 0.176471 0.000000 0.823529 0.000000 0.000000 0.000000 0.000000 1.000000 0.941176 0.000000 0.058824 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.882353 0.000000 0.117647 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.058824 0.000000 0.941176 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.058824 0.000000 0.941176 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 1.000000 0.000000 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 1.000000 0.941176 0.000000 0.000000 0.058824 0.058824 0.000000 0.941176 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCGCGGTATACCGCGGGTTAAAATCTAGT MEME-2 regular expression -------------------------------------------------------------------------------- CCGCGGTATACCGCGGGTTAAAATCTAGT -------------------------------------------------------------------------------- Time 228.69 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************