******************************************************************************** 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/AT5G14960_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/AT5G14960_peak_sequences.fasta -dna -oc out/AT5G14960 -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= 1735 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= 399372 N= 1735 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.304 C 0.196 G 0.196 T 0.304 Background letter frequencies (from file dataset with add-one prior applied): A 0.307 C 0.193 G 0.193 T 0.307 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTCCCGCCAWWWHY MEME-1 width = 15 sites = 1693 llr = 16602 E-value = 2.9e-643 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTCCCGCCAWWWHY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:11:::::655432 pos.-specific C 11:88a:a7111133 probability G 1::12:9:2111111 matrix T 789:::1:1233444 bits 2.4 * * 2.1 * * 1.9 *** 1.7 **** Relative 1.4 ***** Entropy 1.2 ****** (14.1 bits) 0.9 ******** 0.7 ******** 0.5 ********* 0.2 ************* 0.0 --------------- Multilevel TTTCCCGCCAAATTT consensus TTACC sequence AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCCGCCAWWWHY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 375082 bayes= 9.42888 E= 2.9e-643 -101 -95 -108 110 -356 -73 -340 145 -220 -207 -403 151 -247 205 -46 -585 -1737 211 -21 -1737 -1737 237 -1737 -1737 -1737 -635 224 -184 -902 235 -418 -1737 -366 194 -25 -210 98 -57 -150 -64 64 -38 -165 2 77 -65 -114 -20 37 -125 -94 45 -29 39 -127 44 -59 45 -79 45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCCGCCAWWWHY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1693 E= 2.9e-643 0.152392 0.099823 0.091553 0.656232 0.025989 0.116361 0.018311 0.839338 0.066745 0.046072 0.011813 0.875369 0.055523 0.798582 0.140579 0.005316 0.000000 0.833432 0.166568 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.002363 0.911991 0.085647 0.000591 0.988777 0.010632 0.000000 0.024217 0.741288 0.163024 0.071471 0.604253 0.129947 0.068517 0.197283 0.478441 0.148848 0.061429 0.311282 0.521559 0.122859 0.088009 0.267572 0.397519 0.081512 0.101004 0.419965 0.251034 0.252806 0.080331 0.415830 0.204371 0.264028 0.111636 0.419965 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTCCCGCCAWWWHY MEME-1 regular expression -------------------------------------------------------------------------------- TTTCCCGCCA[AT][AT][TA][TCA][TCA] -------------------------------------------------------------------------------- Time 66.21 secs. ******************************************************************************** ******************************************************************************** MOTIF GATTTTAAAAGGKTTTWAAAWGATTTACAAGRGWTTTTAAA MEME-2 width = 41 sites = 46 llr = 1698 E-value = 1.6e-101 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATTTTAAAAGGKTTTWAAAWGATTTACAAGRGWTTTTAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 181::18a7911::::4aaa719:::a:aa:325::::a97 pos.-specific C ::::::1:::::::1::::::::::::9::::::::::::3 probability G 811:::::21975::::::::8::::::::978::::::1: matrix T :18a991:1::15a996:::31:aaa::::1::5aaaa::: bits 2.4 2.1 1.9 * 1.7 * * *** ****** *** Relative 1.4 * * * * * *** ********* ***** Entropy 1.2 * *** * ** *** *** ************ ****** (53.3 bits) 0.9 * ****** *** *** *** ************ ******* 0.7 ******** ************************ ******* 0.5 ***************************************** 0.2 ***************************************** 0.0 ----------------------------------------- Multilevel GATTTTAAAAGGGTTTTAAAAGATTTACAAGGGTTTTTAAA consensus T A T A A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATTTTAAAAGGKTTTWAAAWGATTTACAAGRGWTTTTAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 329972 bayes= 14.3684 E= 1.6e-101 -150 -215 206 -282 135 -215 -115 -182 -223 -1217 -115 147 -1217 -1217 -1217 170 -282 -315 -315 157 -182 -1217 -1217 157 147 -157 -1217 -182 164 -1217 -315 -381 114 -315 -15 -123 154 -1217 -157 -282 -182 -315 220 -1217 -123 -315 193 -150 -282 -1217 131 64 -1217 -315 -315 164 -381 -157 -1217 157 -282 -315 -1217 161 50 -1217 -1217 88 167 -1217 -315 -1217 170 -1217 -1217 -1217 167 -1217 -315 -1217 109 -315 -1217 9 -182 -315 202 -150 161 -1217 -215 -381 -381 -1217 -315 164 -1217 -215 -1217 164 -1217 -315 -1217 167 167 -1217 -1217 -381 -282 224 -1217 -282 167 -1217 -315 -1217 170 -1217 -1217 -1217 -282 -1217 220 -223 9 -1217 175 -381 -82 -315 202 -381 64 -1217 -315 70 -1217 -1217 -1217 170 -1217 -315 -1217 167 -1217 -1217 -1217 170 -282 -1217 -1217 164 164 -1217 -315 -381 150 -1217 -57 -1217 118 55 -315 -1217 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATTTTAAAAGGKTTTWAAAWGATTTACAAGRGWTTTTAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 46 E= 1.6e-101 0.108696 0.043478 0.804348 0.043478 0.782609 0.043478 0.086957 0.086957 0.065217 0.000000 0.086957 0.847826 0.000000 0.000000 0.000000 1.000000 0.043478 0.021739 0.021739 0.913043 0.086957 0.000000 0.000000 0.913043 0.847826 0.065217 0.000000 0.086957 0.956522 0.000000 0.021739 0.021739 0.673913 0.021739 0.173913 0.130435 0.891304 0.000000 0.065217 0.043478 0.086957 0.021739 0.891304 0.000000 0.130435 0.021739 0.739130 0.108696 0.043478 0.000000 0.478261 0.478261 0.000000 0.021739 0.021739 0.956522 0.021739 0.065217 0.000000 0.913043 0.043478 0.021739 0.000000 0.934783 0.434783 0.000000 0.000000 0.565217 0.978261 0.000000 0.021739 0.000000 1.000000 0.000000 0.000000 0.000000 0.978261 0.000000 0.021739 0.000000 0.652174 0.021739 0.000000 0.326087 0.086957 0.021739 0.782609 0.108696 0.934783 0.000000 0.043478 0.021739 0.021739 0.000000 0.021739 0.956522 0.000000 0.043478 0.000000 0.956522 0.000000 0.021739 0.000000 0.978261 0.978261 0.000000 0.000000 0.021739 0.043478 0.913043 0.000000 0.043478 0.978261 0.000000 0.021739 0.000000 1.000000 0.000000 0.000000 0.000000 0.043478 0.000000 0.891304 0.065217 0.326087 0.000000 0.652174 0.021739 0.173913 0.021739 0.782609 0.021739 0.478261 0.000000 0.021739 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.021739 0.000000 0.978261 0.000000 0.000000 0.000000 1.000000 0.043478 0.000000 0.000000 0.956522 0.956522 0.000000 0.021739 0.021739 0.869565 0.000000 0.130435 0.000000 0.695652 0.282609 0.021739 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATTTTAAAAGGKTTTWAAAWGATTTACAAGRGWTTTTAAA MEME-2 regular expression -------------------------------------------------------------------------------- GATTTTAAAAGG[GT]TTT[TA]AAA[AT]GATTTACAAG[GA]G[TA]TTTTAA[AC] -------------------------------------------------------------------------------- Time 126.12 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************