******************************************************************************** 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/AT5G07310_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/AT5G07310_peak_sequences.fasta -dna -oc out/AT5G07310 -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= 5465 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= 1272335 N= 5465 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.261 C 0.239 G 0.239 T 0.261 Background letter frequencies (from file dataset with add-one prior applied): A 0.262 C 0.238 G 0.238 T 0.262 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YCDYCRCCGMCRHHD MEME-1 width = 15 sites = 5456 llr = 44520 E-value = 1.1e-401 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCDYCRCCGMCRHHD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 222113:::314233 pos.-specific C 45159:aa:591331 probability G 1131:6::a::4113 matrix T 3233:1:::2:1433 bits 2.1 *** 1.9 *** 1.7 *** 1.5 * *** * Relative 1.2 * *** * Entropy 1.0 * *** * (11.8 bits) 0.8 ***** * 0.6 ***** * 0.4 ******** 0.2 ** ********** * 0.0 --------------- Multilevel CCTCCGCCGCCATTT consensus TAGT A A GCCA sequence TA T AAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCDYCRCCGMCRHHD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1195825 bayes= 9.70807 E= 1.1e-401 -66 76 -110 29 -16 101 -187 -24 -9 -99 26 41 -149 105 -93 15 -153 189 -436 -391 31 -1906 135 -190 -1906 207 -1906 -848 -890 207 -1906 -1048 -848 -1906 207 -748 -5 103 -274 -21 -183 191 -664 -315 72 -184 75 -140 -17 43 -222 59 6 32 -113 29 18 -164 27 38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCDYCRCCGMCRHHD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5456 E= 1.1e-401 0.166056 0.401393 0.111070 0.321481 0.234238 0.478922 0.065066 0.221774 0.246151 0.119685 0.285374 0.348790 0.093475 0.491202 0.124817 0.290506 0.091092 0.879949 0.011547 0.017412 0.325696 0.000000 0.603922 0.070381 0.000000 0.999267 0.000000 0.000733 0.000550 0.999267 0.000000 0.000183 0.000733 0.000000 0.997801 0.001466 0.252933 0.484238 0.035557 0.227273 0.073680 0.894428 0.002383 0.029509 0.433284 0.066166 0.401026 0.099523 0.232771 0.320381 0.050953 0.395894 0.273094 0.296371 0.108871 0.321664 0.297104 0.076246 0.286290 0.340359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCDYCRCCGMCRHHD MEME-1 regular expression -------------------------------------------------------------------------------- [CT][CAT][TGA][CT]C[GA]CCG[CAT]C[AG][TCA][TCA][TAG] -------------------------------------------------------------------------------- Time 68.44 secs. ******************************************************************************** ******************************************************************************** MOTIF MGRAGRAGRAGRAGA MEME-2 width = 15 sites = 3351 llr = 28097 E-value = 4.8e-108 ******************************************************************************** -------------------------------------------------------------------------------- Motif MGRAGRAGRAGRAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 426636626535717 pos.-specific C 3::2::2::2::1:1 probability G 184274183275:92 matrix T 2::1::1::1::1:: bits 2.1 1.9 1.7 1.5 * Relative 1.2 * * * Entropy 1.0 ** * * * * (12.1 bits) 0.8 ** ** * **** 0.6 ** ** ** ***** 0.4 ******** ***** 0.2 *************** 0.0 --------------- Multilevel AGAAGAAGAAGAAGA consensus CAGCAG G AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGRAGRAGRAGRAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1195825 bayes= 10.5951 E= 4.8e-108 67 21 -91 -53 -24 -1835 168 -397 116 -1835 80 -1835 117 -24 -64 -219 16 -394 151 -408 107 -259 79 -978 126 -33 -167 -131 -76 -1835 181 -442 118 -228 45 -295 103 -33 -61 -114 29 -1835 150 -497 88 -326 102 -469 151 -94 -963 -100 -111 -1835 188 -819 142 -191 -26 -280 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGRAGRAGRAGRAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3351 E= 4.8e-108 0.415995 0.275739 0.126529 0.181737 0.222322 0.000000 0.760967 0.016711 0.586691 0.000000 0.413309 0.000000 0.589078 0.201432 0.152193 0.057296 0.292748 0.015518 0.676216 0.015518 0.550582 0.039391 0.409728 0.000298 0.629961 0.189496 0.074605 0.105939 0.155178 0.000000 0.832587 0.012235 0.592659 0.048941 0.324381 0.034020 0.536556 0.188899 0.155476 0.119069 0.320800 0.000000 0.670845 0.008356 0.483736 0.024769 0.481349 0.010146 0.744852 0.124142 0.000298 0.130707 0.121158 0.000000 0.877947 0.000895 0.700388 0.063265 0.198747 0.037601 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGRAGRAGRAGRAGA MEME-2 regular expression -------------------------------------------------------------------------------- [AC][GA][AG][AC][GA][AG]AG[AG]A[GA][AG]AGA -------------------------------------------------------------------------------- Time 130.03 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************