******************************************************************************** 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/AT5G11260_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/AT5G11260_peak_sequences.fasta -dna -oc out/AT5G11260 -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= 2380 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= 365411 N= 2380 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.302 C 0.198 G 0.198 T 0.302 Background letter frequencies (from file dataset with add-one prior applied): A 0.303 C 0.197 G 0.197 T 0.303 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GRTGACGTGKC MEME-1 width = 11 sites = 2378 llr = 21579 E-value = 1.2e-941 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRTGACGTGKC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 242:a:::112 pos.-specific C :222:a::1:7 probability G 73:7::a:85: matrix T 1161:::a:31 bits 2.3 ** 2.1 ** 1.9 ** 1.6 **** Relative 1.4 **** Entropy 1.2 ***** (13.1 bits) 0.9 ****** * 0.7 * ******** 0.5 * ********* 0.2 * ********* 0.0 ----------- Multilevel GATGACGTGGC consensus G C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRTGACGTGKC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 341611 bayes= 8.43003 E= 1.2e-941 -86 -248 175 -115 34 -11 53 -104 -84 -15 -517 109 -579 15 177 -155 172 -1786 -787 -1786 -1786 234 -787 -579 -749 -1786 234 -1786 -669 -628 -1786 171 -196 -53 195 -354 -139 -587 146 17 -65 178 -311 -151 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRTGACGTGKC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2378 E= 1.2e-941 0.167368 0.035324 0.661060 0.136249 0.385198 0.182506 0.284693 0.147603 0.169470 0.177460 0.005467 0.647603 0.005467 0.217830 0.672834 0.103869 0.999159 0.000000 0.000841 0.000000 0.000000 0.993692 0.000841 0.005467 0.001682 0.000000 0.998318 0.000000 0.002944 0.002523 0.000000 0.994533 0.077796 0.136669 0.759462 0.026072 0.115643 0.003364 0.539529 0.341463 0.193860 0.676619 0.022708 0.106812 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRTGACGTGKC MEME-1 regular expression -------------------------------------------------------------------------------- G[AG]T[GC]ACGTG[GT]C -------------------------------------------------------------------------------- Time 82.02 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTYTTYYTCTTYTTCTTYTY MEME-2 width = 21 sites = 328 llr = 3529 E-value = 6.0e-056 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTYTTYYTCTTYTTCTTYTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 11:111::::1:::::1::1: pos.-specific C 3325235317:3431623524 probability G 111:21:1:2::11:1:::1: matrix T 658366569187569377566 bits 2.3 2.1 1.9 1.6 Relative 1.4 * * Entropy 1.2 ** * (15.5 bits) 0.9 * **** * ** 0.7 * ******* ***** * 0.5 * ** **************** 0.2 ********************* 0.0 --------------------- Multilevel TTTCTTTTTCTTTTTCTTTTT consensus CC T CCC CCC T CCCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTTYYTCTTYTTCTTYTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 317811 bayes= 12.1076 E= 6.0e-056 -194 46 -115 89 -151 63 -137 76 -431 -23 -176 132 -114 141 -301 5 -164 -13 -28 89 -199 46 -192 99 -405 124 -1500 77 -1500 62 -73 93 -1500 -126 -1500 160 -1500 191 -23 -168 -105 -231 -443 141 -318 60 -1500 114 -405 119 -149 61 -264 40 -143 103 -1500 -115 -1500 159 -273 165 -131 -24 -183 -15 -284 123 -1500 59 -1500 122 -405 128 -601 72 -231 27 -176 108 -305 87 -401 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTTYYTCTTYTTCTTYTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 328 E= 6.0e-056 0.079268 0.271341 0.088415 0.560976 0.106707 0.304878 0.076220 0.512195 0.015244 0.167683 0.057927 0.759146 0.137195 0.524390 0.024390 0.314024 0.097561 0.179878 0.161585 0.560976 0.076220 0.271341 0.051829 0.600610 0.018293 0.463415 0.000000 0.518293 0.000000 0.301829 0.118902 0.579268 0.000000 0.082317 0.000000 0.917683 0.000000 0.737805 0.167683 0.094512 0.146341 0.039634 0.009146 0.804878 0.033537 0.298780 0.000000 0.667683 0.018293 0.448171 0.070122 0.463415 0.048780 0.259146 0.073171 0.618902 0.000000 0.088415 0.000000 0.911585 0.045732 0.618902 0.079268 0.256098 0.085366 0.176829 0.027439 0.710366 0.000000 0.295732 0.000000 0.704268 0.018293 0.478659 0.003049 0.500000 0.060976 0.237805 0.057927 0.643293 0.036585 0.359756 0.012195 0.591463 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTTYYTCTTYTTCTTYTY MEME-2 regular expression -------------------------------------------------------------------------------- [TC][TC]T[CT]T[TC][TC][TC]TCT[TC][TC][TC]T[CT]T[TC][TC][TC][TC] -------------------------------------------------------------------------------- Time 153.19 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************