******************************************************************************** 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/AT5G02460_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/AT5G02460_peak_sequences.fasta -dna -oc out/AT5G02460 -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= 6174 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= 1554522 N= 6174 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.362 C 0.138 G 0.138 T 0.362 Background letter frequencies (from file dataset with add-one prior applied): A 0.362 C 0.138 G 0.138 T 0.362 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DAAAAAAAAAAAAARAAAAAG MEME-1 width = 21 sites = 5351 llr = 44043 E-value = 1.8e-178 ******************************************************************************** -------------------------------------------------------------------------------- Motif DAAAAAAAAAAAAARAAAAAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 456656777887565889992 pos.-specific C 111111111:::1111::::: probability G 2222222122123231111:8 matrix T 32112111::1:121:1::1: bits 2.9 2.6 2.3 2.0 * Relative 1.7 * Entropy 1.4 * (11.9 bits) 1.1 * ** * 0.9 * ***** 0.6 * **** ****** 0.3 ******************* 0.0 --------------------- Multilevel AAAAAAAAAAAAAAAAAAAAG consensus T G G GG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAAAAAAAAAAAAARAAAAAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1431042 bayes= 10.252 E= 1.8e-178 9 0 53 -38 45 8 32 -96 61 -53 64 -142 62 -28 40 -130 58 -2 17 -111 62 -12 54 -163 88 -92 47 -236 94 -136 4 -174 102 -117 21 -309 121 -672 17 -667 106 -231 -3 -214 94 -197 77 -338 59 -35 93 -210 65 -60 34 -110 44 -24 88 -138 109 -34 -49 -418 123 -279 -106 -244 134 -453 -89 -1903 134 -255 -116 -1903 134 -330 -281 -281 -98 -536 256 -860 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAAAAAAAAAAAAARAAAAAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5351 E= 1.8e-178 0.384788 0.138292 0.198468 0.278453 0.494861 0.146141 0.172304 0.186694 0.554476 0.095683 0.214726 0.135115 0.557466 0.113624 0.181461 0.147449 0.541768 0.136049 0.154924 0.167258 0.555223 0.127079 0.200336 0.117361 0.665109 0.072884 0.191553 0.070454 0.695945 0.053822 0.141656 0.108578 0.736498 0.061297 0.159783 0.042422 0.839656 0.001308 0.155485 0.003551 0.755373 0.027845 0.134741 0.082041 0.694823 0.035321 0.235096 0.034760 0.543824 0.108204 0.263315 0.084657 0.566436 0.090824 0.174360 0.168380 0.490563 0.116801 0.253971 0.138666 0.772566 0.109138 0.098299 0.019996 0.846944 0.019996 0.066156 0.066903 0.919454 0.005980 0.074566 0.000000 0.914595 0.023547 0.061858 0.000000 0.914595 0.014016 0.019623 0.051766 0.183891 0.003364 0.811811 0.000934 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAAAAAAAAAAAAARAAAAAG MEME-1 regular expression -------------------------------------------------------------------------------- [AT]A[AG]AA[AG]AAAAA[AG][AG]A[AG]AAAAAG -------------------------------------------------------------------------------- Time 75.77 secs. ******************************************************************************** ******************************************************************************** MOTIF TTWACTTTTTN MEME-2 width = 11 sites = 6170 llr = 40650 E-value = 1.4e-051 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTWACTTTTTN MEME-2 Description -------------------------------------------------------------------------------- Simplified A 2145::::113 pos.-specific C 1222a::::12 probability G 11:1:::::12 matrix T 6641:aaa973 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.5 bits) 1.1 **** 0.9 ***** 0.6 ****** 0.3 ** ******* 0.0 ----------- Multilevel TTTACTTTTTT consensus CAC A sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWACTTTTTN MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1492782 bayes= 9.92501 E= 1.4e-051 -102 -64 -17 75 -178 66 -117 77 0 38 -194 22 46 76 -11 -134 -1923 284 -503 -580 -1923 -641 -673 146 -912 -1923 -1923 146 -1923 -593 -1923 146 -221 -318 -656 132 -245 -23 -77 102 -42 59 81 -37 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWACTTTTTN MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6170 E= 1.4e-051 0.179092 0.088493 0.122528 0.609887 0.105348 0.217666 0.061426 0.615559 0.363209 0.179254 0.035818 0.421718 0.496596 0.232739 0.128039 0.142626 0.000000 0.989303 0.004214 0.006483 0.000000 0.001621 0.001297 0.997083 0.000648 0.000000 0.000000 0.999352 0.000000 0.002269 0.000000 0.997731 0.078120 0.015235 0.001459 0.905186 0.066451 0.117180 0.080713 0.735656 0.271151 0.207293 0.242301 0.279254 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTWACTTTTTN MEME-2 regular expression -------------------------------------------------------------------------------- T[TC][TA][AC]CTTTTT[TAGC] -------------------------------------------------------------------------------- Time 144.00 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 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