******************************************************************************** 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/AT1G12260_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/AT1G12260_peak_sequences.fasta -dna -oc out/AT1G12260 -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= 6306 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= 1400139 N= 6306 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.322 C 0.178 G 0.178 T 0.322 Background letter frequencies (from file dataset with add-one prior applied): A 0.323 C 0.177 G 0.177 T 0.323 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTNCTTNWWYTWYAMGYHWHH MEME-1 width = 21 sites = 6230 llr = 51131 E-value = 4.5e-399 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTNCTTNWWYTWYAMGYHWHH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 223:::2331221a5:13622 pos.-specific C :129::2223224:5:42:34 probability G :13:2:4221111::81::11 matrix T 863:8a2444544::244433 bits 2.5 2.3 2.0 * 1.8 * Relative 1.5 * * * * Entropy 1.3 * * * * (11.8 bits) 1.0 *** *** 0.8 * *** *** 0.5 * *** **** * 0.3 ** **** * ********* 0.0 --------------------- Multilevel TTGCTTGTTTTTCACGTTATC consensus AT G CAACCAT ATCATCT sequence A A C AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTNWWYTWYAMGYHWHH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1274019 bayes= 9.77668 E= 4.5e-399 -84 -223 -366 125 -42 -159 -25 77 -30 -10 78 -26 -309 237 -730 -283 -1925 -1925 33 127 -1925 -602 -353 160 -57 41 103 -78 -11 -11 -11 21 -32 8 -5 25 -111 63 -34 44 -85 24 -37 56 -38 4 -50 46 -240 126 -76 35 161 -376 -1010 -1097 59 153 -1925 -781 -997 -1925 216 -63 -136 109 -106 36 10 25 -235 34 89 -395 -384 22 -54 94 -95 10 -56 110 -25 -35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTNWWYTWYAMGYHWHH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6230 E= 4.5e-399 0.181220 0.037721 0.013965 0.767095 0.242215 0.058748 0.148475 0.550562 0.262279 0.165169 0.302247 0.270305 0.038042 0.915409 0.001124 0.045425 0.000000 0.000000 0.222632 0.777368 0.000000 0.002729 0.015249 0.982022 0.217817 0.233868 0.360032 0.188283 0.299839 0.163082 0.163242 0.373836 0.258587 0.186998 0.170144 0.384270 0.149599 0.272552 0.139968 0.437881 0.178812 0.208347 0.136437 0.476404 0.248636 0.181220 0.125040 0.445104 0.061477 0.421830 0.104494 0.412199 0.986677 0.013002 0.000161 0.000161 0.488283 0.510273 0.000000 0.001445 0.000321 0.000000 0.790048 0.209631 0.125843 0.375441 0.084591 0.414125 0.346067 0.209952 0.034671 0.409310 0.598716 0.011396 0.012360 0.377528 0.222151 0.339968 0.091332 0.346549 0.220064 0.377689 0.148475 0.253772 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTNWWYTWYAMGYHWHH MEME-1 regular expression -------------------------------------------------------------------------------- T[TA][GTA]C[TG]T[GCA][TA][TA][TC][TC][TA][CT]A[CA][GT][TC][TAC][AT][TCA][CTA] -------------------------------------------------------------------------------- Time 127.23 secs. ******************************************************************************** ******************************************************************************** MOTIF RRAGARRAAGAARAARARAAR MEME-2 width = 21 sites = 810 llr = 9221 E-value = 1.4e-037 ******************************************************************************** -------------------------------------------------------------------------------- Motif RRAGARRAAGAARAARARAAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 467395589387586475754 pos.-specific C 111::1::111:::111:111 probability G 5327:352:6:2523414233 matrix T ::::11:::::::::11::11 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 * * (16.4 bits) 1.0 ** ****** 0.8 ***** ********* ** 0.5 ******************* 0.3 ********************* 0.0 --------------------- Multilevel GAAGAAAAAGAAGAAAAAAAA consensus AG A GGG A GA GG GGGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAGARRAAGAARAARARAAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1274019 bayes= 12.9127 E= 1.4e-037 47 -173 150 -1631 86 -59 75 -1631 112 -67 2 -545 4 -1631 192 -1631 144 -1631 -299 -171 68 -59 80 -251 59 -191 141 -1631 123 -1631 44 -803 148 -155 -225 -803 -17 -149 188 -1631 137 -67 -246 -413 118 -1631 50 -403 59 -1631 154 -1631 126 -270 -16 -303 92 -95 75 -1631 39 -161 120 -153 116 -37 -107 -251 70 -1631 131 -308 108 -141 49 -1631 74 -52 54 -201 22 -29 96 -126 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAGARRAAGAARAARARAAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 810 E= 1.4e-037 0.446914 0.053086 0.500000 0.000000 0.586420 0.117284 0.296296 0.000000 0.702469 0.111111 0.179012 0.007407 0.332099 0.000000 0.667901 0.000000 0.879012 0.000000 0.022222 0.098765 0.518519 0.117284 0.307407 0.056790 0.485185 0.046914 0.467901 0.000000 0.759259 0.000000 0.239506 0.001235 0.901235 0.060494 0.037037 0.001235 0.287654 0.062963 0.649383 0.000000 0.838272 0.111111 0.032099 0.018519 0.730864 0.000000 0.249383 0.019753 0.487654 0.000000 0.512346 0.000000 0.775309 0.027160 0.158025 0.039506 0.611111 0.091358 0.297531 0.000000 0.424691 0.058025 0.404938 0.112346 0.722222 0.137037 0.083951 0.056790 0.524691 0.000000 0.437037 0.038272 0.685185 0.066667 0.248148 0.000000 0.539506 0.123457 0.256790 0.080247 0.377778 0.144444 0.343210 0.134568 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAGARRAAGAARAARARAAR MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG]A[GA]A[AG][AG][AG]A[GA]A[AG][GA]A[AG][AG]A[AG][AG][AG][AG] -------------------------------------------------------------------------------- Time 237.12 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************