******************************************************************************** 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/AT5G65210_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/AT5G65210_peak_sequences.fasta -dna -oc out/AT5G65210 -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= 5018 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= 994623 N= 5018 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.308 C 0.192 G 0.192 T 0.308 Background letter frequencies (from file dataset with add-one prior applied): A 0.31 C 0.19 G 0.19 T 0.31 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NNYBACGTCATCWWH MEME-1 width = 15 sites = 4978 llr = 41430 E-value = 1.3e-493 ******************************************************************************** -------------------------------------------------------------------------------- Motif NNYBACGTCATCWWH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33219:1:1a:1432 pos.-specific C 2233:a::9:26123 probability G 33:3::9:::21211 matrix T 32531::a::62344 bits 2.4 2.2 * 1.9 * * 1.7 ***** Relative 1.4 ***** Entropy 1.2 ***** (12.0 bits) 1.0 ****** 0.7 ****** * 0.5 ******** 0.2 ********** 0.0 --------------- Multilevel GGTGACGTCATCATT consensus TACT G TAC sequence ATAC C A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NNYBACGTCATCWWH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 924371 bayes= 9.84788 E= 1.3e-493 -30 -31 69 -10 -20 13 63 -45 -58 64 -245 58 -176 57 86 -13 148 -503 -204 -186 -1059 232 -756 -268 -133 -362 218 -1893 -1893 -1893 -1893 169 -208 229 -1893 -1893 169 -1893 -1893 -1893 -627 16 28 83 -127 169 -109 -87 44 -41 -26 -16 -1 -19 -62 37 -35 65 -81 18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NNYBACGTCATCWWH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4978 E= 1.3e-493 0.252109 0.153676 0.305946 0.288268 0.270390 0.208718 0.293692 0.227200 0.207915 0.295500 0.034753 0.461832 0.091603 0.281840 0.344114 0.282443 0.862796 0.005826 0.046203 0.085175 0.000201 0.950382 0.001004 0.048413 0.123142 0.015468 0.861390 0.000000 0.000000 0.000000 0.000000 1.000000 0.073323 0.926677 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.004018 0.212937 0.231016 0.552029 0.128767 0.612696 0.089192 0.169345 0.419847 0.142828 0.159100 0.278224 0.308156 0.166734 0.123744 0.401366 0.242668 0.298915 0.108076 0.350342 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NNYBACGTCATCWWH MEME-1 regular expression -------------------------------------------------------------------------------- [GTA][GATC][TCA][GTC]ACGTCA[TGC]C[AT][TA][TCA] -------------------------------------------------------------------------------- Time 76.88 secs. ******************************************************************************** ******************************************************************************** MOTIF YTCTYYYTCTYYYTCTYYYYY MEME-2 width = 21 sites = 610 llr = 7289 E-value = 8.4e-028 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTCTYYYTCTYYYTCTYYYYY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:::::1::1::1::1:1:11 pos.-specific C 418:45338154327146336 probability G :::2:11::1::2::1::2:: matrix T 592854571755483753553 bits 2.4 2.2 1.9 1.7 Relative 1.4 * Entropy 1.2 *** * * (17.2 bits) 1.0 *** ** * ** ** 0.7 ***** ** ** ** ** * 0.5 ****** ***** ******** 0.2 ********************* 0.0 --------------------- Multilevel TTCTTCTTCTCTTTCTTCTTC consensus C T CTCC TCCCT CTCCT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCTYYYTCTYYYTCTYYYYY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 894263 bayes= 12.802 E= 8.4e-028 -122 103 -1590 63 -1590 -63 -1590 150 -410 200 -1590 -48 -1590 -1590 -26 144 -1590 121 -221 74 -375 140 -181 45 -148 65 -140 74 -756 44 -1590 126 -366 206 -254 -107 -173 -130 -110 126 -1590 141 -1590 67 -317 115 -254 72 -189 81 -33 48 -1590 33 -1590 130 -375 185 -1590 -9 -150 -110 -105 120 -410 124 -685 78 -214 164 -1590 12 -424 64 12 63 -139 88 -1590 78 -261 163 -227 6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCTYYYTCTYYYTCTYYYYY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 610 E= 8.4e-028 0.132787 0.386885 0.000000 0.480328 0.000000 0.122951 0.000000 0.877049 0.018033 0.759016 0.000000 0.222951 0.000000 0.000000 0.159016 0.840984 0.000000 0.440984 0.040984 0.518033 0.022951 0.500000 0.054098 0.422951 0.111475 0.298361 0.072131 0.518033 0.001639 0.257377 0.000000 0.740984 0.024590 0.795082 0.032787 0.147541 0.093443 0.077049 0.088525 0.740984 0.000000 0.506557 0.000000 0.493443 0.034426 0.421311 0.032787 0.511475 0.083607 0.334426 0.150820 0.431148 0.000000 0.239344 0.000000 0.760656 0.022951 0.685246 0.000000 0.291803 0.109836 0.088525 0.091803 0.709836 0.018033 0.449180 0.001639 0.531148 0.070492 0.593443 0.000000 0.336066 0.016393 0.296721 0.206557 0.480328 0.118033 0.349180 0.000000 0.532787 0.050820 0.586885 0.039344 0.322951 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCTYYYTCTYYYTCTYYYYY MEME-2 regular expression -------------------------------------------------------------------------------- [TC]T[CT]T[TC][CT][TC][TC]CT[CT][TC][TC][TC][CT]T[TC][CT][TCG][TC][CT] -------------------------------------------------------------------------------- Time 140.93 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************