******************************************************************************** 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/AT3G56400_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/AT3G56400_peak_sequences.fasta -dna -oc out/AT3G56400 -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= 4974 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= 1033894 N= 4974 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.322 C 0.178 G 0.178 T 0.322 Background letter frequencies (from file dataset with add-one prior applied): A 0.324 C 0.176 G 0.176 T 0.324 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NMGTTGACTT MEME-1 width = 10 sites = 4969 llr = 41292 E-value = 2.2e-495 ******************************************************************************** -------------------------------------------------------------------------------- Motif NMGTTGACTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 321:::a::2 pos.-specific C 25:::::a21 probability G 218::a:::1 matrix T 321aa:::76 bits 2.5 * * 2.3 * * 2.0 * * 1.8 * * Relative 1.5 ***** Entropy 1.3 ****** (12.0 bits) 1.0 ****** 0.8 ******* 0.5 ******* 0.3 ********* 0.0 ---------- Multilevel TCGTTGACTT consensus AA CA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NMGTTGACTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 989128 bayes= 9.48061 E= 2.2e-495 -32 3 44 -1 -45 137 -37 -91 -123 -219 212 -240 -424 -452 -877 159 -465 -538 -428 159 -1892 -1892 250 -665 163 -1892 -1892 -1892 -785 250 -1892 -865 -363 50 -323 112 -41 -69 -164 86 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NMGTTGACTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 4969 E= 2.2e-495 0.258805 0.180117 0.238881 0.322198 0.236869 0.453612 0.136446 0.173073 0.137855 0.038438 0.762326 0.061381 0.017106 0.007647 0.000402 0.974844 0.012880 0.004226 0.009056 0.973838 0.000000 0.000000 0.996780 0.003220 1.000000 0.000000 0.000000 0.000000 0.001409 0.997786 0.000000 0.000805 0.026162 0.248943 0.018716 0.706178 0.244114 0.109278 0.056551 0.590058 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NMGTTGACTT MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][CA]GTTGAC[TC][TA] -------------------------------------------------------------------------------- Time 75.30 secs. ******************************************************************************** ******************************************************************************** MOTIF TWTWWWWYGWCCMAWWTTTGAAAGTTSGSGNWTTWWWTGACATTTTTCC MEME-2 width = 49 sites = 22 llr = 909 E-value = 5.6e-030 ******************************************************************************** -------------------------------------------------------------------------------- Motif TWTWWWWYGWCCMAWWTTTGAAAGTTSGSGNWTTWWWTGACATTTTTCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 24:4565:14::5555::::aaa::::31:46:1454:29:a1:::::: pos.-specific C 1::::::5::8a52::::::::::::6:5:2::::::2::a:::::1a8 probability G ::::1:::8:::::::::19:::a::373a2:::::::81::::::::: matrix T 66a64455:61::255aa9:::::aa::2:24a96568::::9aaa9:1 bits 2.5 * 2.3 * * * * * 2.0 * * * * * * 1.8 * * * * * * Relative 1.5 * * ** * ******* * * ** *** ** Entropy 1.3 * * ** ************ * * *********** (59.6 bits) 1.0 * ** *** ************ * ** ************ 0.8 *** * ****** ************* * ***** ************ 0.5 **** ************************* ****************** 0.3 ****************************** ****************** 0.0 ------------------------------------------------- Multilevel TTTTAAACGTCCCAAATTTGAAAGTTCGCGAATTTTTTGACATTTTTCC consensus AA ATTTT A ACTT GAG GT AAA sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWTWWWWYGWCCMAWWTTTGAAAGTTSGSGNWTTWWWTGACATTTTTCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 49 n= 795142 bayes= 15.4965 E= 5.6e-030 -51 -37 -1110 97 34 -1110 -1110 87 -1110 -1110 -1110 163 34 -1110 -1110 87 63 -1110 -95 34 97 -1110 -1110 17 63 -195 -1110 49 -1110 163 -1110 49 -125 -195 222 -1110 34 -1110 -1110 87 -283 222 -195 -183 -1110 244 -1110 -283 49 151 -195 -1110 75 37 -1110 -51 63 -1110 -1110 63 75 -1110 -1110 49 -1110 -1110 -1110 163 -283 -1110 -1110 156 -1110 -1110 -95 149 -1110 -195 237 -283 163 -1110 -1110 -1110 163 -1110 -1110 -1110 156 -1110 -195 -1110 -283 -1110 244 -1110 -1110 -1110 -1110 163 -1110 -1110 -1110 163 -283 185 85 -1110 -3 -1110 195 -1110 -183 137 63 -83 -1110 -1110 251 -1110 17 5 37 -51 87 -1110 -1110 34 -1110 -1110 -1110 163 -125 -1110 -1110 141 34 -1110 -1110 87 49 -1110 -1110 75 17 -195 -1110 87 -1110 5 -1110 134 -83 -1110 213 -283 149 -1110 -95 -1110 -283 244 -1110 -1110 156 -195 -1110 -1110 -183 -1110 -1110 149 -1110 -1110 -1110 163 -1110 -1110 -1110 163 -1110 -1110 -1110 163 -1110 -37 -1110 141 -1110 244 -1110 -283 -283 222 -195 -183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWTWWWWYGWCCMAWWTTTGAAAGTTSGSGNWTTWWWTGACATTTTTCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 49 nsites= 22 E= 5.6e-030 0.227273 0.136364 0.000000 0.636364 0.409091 0.000000 0.000000 0.590909 0.000000 0.000000 0.000000 1.000000 0.409091 0.000000 0.000000 0.590909 0.500000 0.000000 0.090909 0.409091 0.636364 0.000000 0.000000 0.363636 0.500000 0.045455 0.000000 0.454545 0.000000 0.545455 0.000000 0.454545 0.136364 0.045455 0.818182 0.000000 0.409091 0.000000 0.000000 0.590909 0.045455 0.818182 0.045455 0.090909 0.000000 0.954545 0.000000 0.045455 0.454545 0.500000 0.045455 0.000000 0.545455 0.227273 0.000000 0.227273 0.500000 0.000000 0.000000 0.500000 0.545455 0.000000 0.000000 0.454545 0.000000 0.000000 0.000000 1.000000 0.045455 0.000000 0.000000 0.954545 0.000000 0.000000 0.090909 0.909091 0.000000 0.045455 0.909091 0.045455 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.954545 0.000000 0.045455 0.000000 0.045455 0.000000 0.954545 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.045455 0.636364 0.318182 0.000000 0.318182 0.000000 0.681818 0.000000 0.090909 0.454545 0.272727 0.181818 0.000000 0.000000 1.000000 0.000000 0.363636 0.181818 0.227273 0.227273 0.590909 0.000000 0.000000 0.409091 0.000000 0.000000 0.000000 1.000000 0.136364 0.000000 0.000000 0.863636 0.409091 0.000000 0.000000 0.590909 0.454545 0.000000 0.000000 0.545455 0.363636 0.045455 0.000000 0.590909 0.000000 0.181818 0.000000 0.818182 0.181818 0.000000 0.772727 0.045455 0.909091 0.000000 0.090909 0.000000 0.045455 0.954545 0.000000 0.000000 0.954545 0.045455 0.000000 0.000000 0.090909 0.000000 0.000000 0.909091 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 0.136364 0.000000 0.863636 0.000000 0.954545 0.000000 0.045455 0.045455 0.818182 0.045455 0.090909 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TWTWWWWYGWCCMAWWTTTGAAAGTTSGSGNWTTWWWTGACATTTTTCC MEME-2 regular expression -------------------------------------------------------------------------------- [TA][TA]T[TA][AT][AT][AT][CT]G[TA]CC[CA][ACT][AT][AT]TTTGAAAGTT[CG][GA][CG]G[AGT][AT]TT[TA][TA][TA]TGACATTTTTCC -------------------------------------------------------------------------------- Time 133.50 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************