******************************************************************************** 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/AT5G65410_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/AT5G65410_peak_sequences.fasta -dna -oc out/AT5G65410 -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= 5777 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= 1690465 N= 5777 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.386 C 0.114 G 0.114 T 0.386 Background letter frequencies (from file dataset with add-one prior applied): A 0.386 C 0.114 G 0.114 T 0.386 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TSMCHAAVHCTCTCCMHMWHMMBBACMCG MEME-1 width = 29 sites = 292 llr = 3769 E-value = 7.3e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSMCHAAVHCTCTCCMHMWHMMBBACMCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:333663322121:4343243:151522 pos.-specific C 25473214362627644423444317361 probability G 142:1212:121111111:1112411215 matrix T 611:3:21415251312154124321112 bits 3.1 2.8 2.5 2.2 Relative 1.9 Entropy 1.6 * * (18.6 bits) 1.3 * * ** * 0.9 * * * * ** * * * 0.6 *** * * * * ** ** *** * ** 0.3 **** * *********** **** **** 0.0 ----------------------------- Multilevel TCCCTAACTCTCTCCACCTTCCCGACACG consensus CGAAACTACA C TCAAACAATTT C A sequence CG GA T A GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSMCHAAVHCTCTCCMHMWHMMBBACMCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 1528708 bayes= 14.599 E= 7.3e-011 -236 103 3 58 -681 206 181 -169 -59 191 80 -173 -41 255 -160 -681 -41 117 -6 -17 60 87 85 -1483 53 30 -36 -86 -31 166 103 -201 -57 154 -1483 8 -67 227 -73 -149 -123 53 62 36 -146 236 7 -132 -109 85 -41 45 -191 262 -115 -139 -1483 239 30 -55 13 167 -25 -169 -46 194 -89 -82 9 186 -53 -201 -17 56 -189 25 -65 115 -10 3 -13 180 -10 -142 -63 195 37 -126 -1483 180 85 4 -273 132 164 -36 43 37 -1 -82 -165 259 -36 -191 23 135 43 -191 -112 242 -10 -186 -93 37 207 -117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSMCHAAVHCTCTCCMHMWHMMBBACMCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 292 E= 7.3e-011 0.075342 0.232877 0.116438 0.575342 0.003425 0.476027 0.400685 0.119863 0.256849 0.428082 0.198630 0.116438 0.291096 0.667808 0.037671 0.003425 0.291096 0.256849 0.109589 0.342466 0.585616 0.208904 0.205479 0.000000 0.558219 0.140411 0.089041 0.212329 0.311644 0.359589 0.232877 0.095890 0.260274 0.332192 0.000000 0.407534 0.243151 0.551370 0.068493 0.136986 0.164384 0.164384 0.174658 0.496575 0.140411 0.585616 0.119863 0.154110 0.181507 0.205479 0.085616 0.527397 0.102740 0.698630 0.051370 0.147260 0.000000 0.595890 0.140411 0.263699 0.421233 0.363014 0.095890 0.119863 0.280822 0.438356 0.061644 0.219178 0.410959 0.414384 0.078767 0.095890 0.342466 0.167808 0.030822 0.458904 0.246575 0.253425 0.106164 0.393836 0.352740 0.397260 0.106164 0.143836 0.250000 0.441781 0.147260 0.160959 0.000000 0.397260 0.205479 0.397260 0.058219 0.284247 0.356164 0.301370 0.520548 0.147260 0.113014 0.219178 0.123288 0.684932 0.089041 0.102740 0.452055 0.291096 0.154110 0.102740 0.178082 0.609589 0.106164 0.106164 0.202055 0.147260 0.479452 0.171233 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSMCHAAVHCTCTCCMHMWHMMBBACMCG MEME-1 regular expression -------------------------------------------------------------------------------- [TC][CG][CA][CA][TAC][ACG][AT][CAG][TCA][CA]TC[TC]C[CT][AC][CAT][CA][TA][TCA][CA][CA][CTG][GTC][AT]C[AC]C[GA] -------------------------------------------------------------------------------- Time 73.68 secs. ******************************************************************************** ******************************************************************************** MOTIF AAAATATTTAGACAATRATTCATAAACATATCATAAATAAGATCAACATT MEME-2 width = 50 sites = 44 llr = 2202 E-value = 5.3e-017 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAATATTTAGACAATRATTCATAAACATATCATAAATAAGATCAACATT MEME-2 Description -------------------------------------------------------------------------------- Simplified A aaaa:a:::a1a:aa:5a:::a:aa9:a:a::a:aaa:aa2a::a9:91: pos.-specific C ::::::::::::9:::::::9:::::a::::9:::::::::::8::8::: probability G ::::::::::9:::::5:::::::::::::::::::::::8::::1:1:: matrix T ::::a:aaa:::1::a::aa1:a:::::a:a1:a:::a::::a2::2:99 bits 3.1 2.8 * 2.5 * * * * 2.2 * * * * * * * Relative 1.9 * * * * * * * * Entropy 1.6 * * * * * * * * (72.2 bits) 1.3 ************************* ******************* * 0.9 ************************************************** 0.6 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel AAAATATTTAGACAATAATTCATAAACATATCATAAATAAGATCAACATT consensus G T T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATATTTAGACAATRATTCATAAACATATCATAAATAAGATCAACATT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 1407391 bayes= 16.4986 E= 5.3e-017 137 -1210 -1210 -1210 137 -1210 -1210 -1210 134 -1210 -1210 -408 137 -1210 -1210 -1210 -1210 -1210 -1210 137 131 -1210 -133 -1210 -408 -1210 -1210 134 -1210 -1210 -1210 137 -408 -1210 -1210 134 131 -1210 -1210 -308 -250 -1210 296 -308 137 -1210 -1210 -1210 -1210 300 -1210 -209 134 -1210 -1210 -408 137 -1210 -1210 -1210 -1210 -1210 -1210 137 44 -1210 207 -1210 134 -1210 -233 -1210 -1210 -1210 -1210 137 -1210 -1210 -1210 137 -1210 300 -1210 -209 137 -1210 -1210 -1210 -1210 -1210 -233 134 134 -233 -1210 -1210 134 -1210 -233 -1210 127 -1210 -133 -408 -408 307 -1210 -408 134 -1210 -233 -1210 -1210 -1210 -1210 137 137 -1210 -1210 -1210 -1210 -1210 -1210 137 -1210 300 -233 -250 137 -1210 -1210 -1210 -1210 -1210 -233 134 137 -1210 -1210 -1210 137 -1210 -1210 -1210 134 -1210 -233 -1210 -1210 -1210 -1210 137 137 -1210 -1210 -1210 137 -1210 -1210 -1210 -109 -1210 284 -1210 134 -1210 -233 -1210 -1210 -1210 -1210 137 -1210 280 -1210 -92 137 -1210 -1210 -1210 120 -233 -33 -1210 -408 276 -1210 -92 124 -1210 -74 -408 -250 -1210 -1210 127 -408 -233 -133 124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATATTTAGACAATRATTCATAAACATATCATAAATAAGATCAACATT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 44 E= 5.3e-017 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.977273 0.000000 0.000000 0.022727 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.954545 0.000000 0.045455 0.000000 0.022727 0.000000 0.000000 0.977273 0.000000 0.000000 0.000000 1.000000 0.022727 0.000000 0.000000 0.977273 0.954545 0.000000 0.000000 0.045455 0.068182 0.000000 0.886364 0.045455 1.000000 0.000000 0.000000 0.000000 0.000000 0.909091 0.000000 0.090909 0.977273 0.000000 0.000000 0.022727 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.522727 0.000000 0.477273 0.000000 0.977273 0.000000 0.022727 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.909091 0.000000 0.090909 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.022727 0.977273 0.977273 0.022727 0.000000 0.000000 0.977273 0.000000 0.022727 0.000000 0.931818 0.000000 0.045455 0.022727 0.022727 0.954545 0.000000 0.022727 0.977273 0.000000 0.022727 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.909091 0.022727 0.068182 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.022727 0.977273 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.977273 0.000000 0.022727 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.181818 0.000000 0.818182 0.000000 0.977273 0.000000 0.022727 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.795455 0.000000 0.204545 1.000000 0.000000 0.000000 0.000000 0.886364 0.022727 0.090909 0.000000 0.022727 0.772727 0.000000 0.204545 0.909091 0.000000 0.068182 0.022727 0.068182 0.000000 0.000000 0.931818 0.022727 0.022727 0.045455 0.909091 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAATATTTAGACAATRATTCATAAACATATCATAAATAAGATCAACATT MEME-2 regular expression -------------------------------------------------------------------------------- AAAATATTTAGACAAT[AG]ATTCATAAACATATCATAAATAAGAT[CT]AA[CT]ATT -------------------------------------------------------------------------------- Time 143.27 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************