******************************************************************************** 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/AT3G12730_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/AT3G12730_peak_sequences.fasta -dna -oc out/AT3G12730 -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= 8522 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= 1712623 N= 8522 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.336 C 0.164 G 0.164 T 0.336 Background letter frequencies (from file dataset with add-one prior applied): A 0.337 C 0.163 G 0.163 T 0.337 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAKATTCYHTW MEME-1 width = 11 sites = 8503 llr = 60191 E-value = 5.5e-243 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAKATTCYHTW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 58:a::::223 pos.-specific C 1:::::a3221 probability G 1:7::::2111 matrix T 223:aa:5455 bits 2.6 * 2.4 * 2.1 * 1.8 * Relative 1.6 ** * Entropy 1.3 ***** (10.2 bits) 1.0 ***** 0.8 ****** 0.5 ******* 0.3 ******* 0.0 ----------- Multilevel AAGATTCTTTT consensus T T CAAA sequence GC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAKATTCYHTW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1627403 bayes= 9.59075 E= 5.5e-243 60 -13 -73 -47 127 -406 -388 -102 -816 -1043 201 2 156 -585 -1970 -990 -1148 -1970 -1970 157 -648 -558 -406 154 -1970 262 -1970 -1970 -948 92 40 50 -57 45 -61 39 -49 25 -93 52 -42 -23 -47 55 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAKATTCYHTW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 8503 E= 5.5e-243 0.509232 0.148889 0.097965 0.243914 0.813125 0.009761 0.011055 0.166059 0.001176 0.000118 0.656121 0.342585 0.996825 0.002823 0.000000 0.000353 0.000118 0.000000 0.000000 0.999882 0.003763 0.003411 0.009761 0.983065 0.000000 1.000000 0.000000 0.000000 0.000470 0.309067 0.214630 0.475832 0.227214 0.222863 0.106903 0.443020 0.239210 0.193579 0.085264 0.481948 0.251205 0.138539 0.117606 0.492650 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAKATTCYHTW MEME-1 regular expression -------------------------------------------------------------------------------- [AT]A[GT]ATTC[TCG][TAC][TA][TA] -------------------------------------------------------------------------------- Time 71.77 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTTYTTYTTYTTYTTTTTYT MEME-2 width = 21 sites = 2006 llr = 19170 E-value = 3.2e-012 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTYTTTTTYT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21::22::::1:1::::11:1 pos.-specific C 132232:5:133:5:232131 probability G 1112:::1:21:::11:1122 matrix T 658656949757959776856 bits 2.6 2.4 2.1 1.8 Relative 1.6 Entropy 1.3 * (13.8 bits) 1.0 * * **** * 0.8 * **** ****** 0.5 *** **** ********* 0.3 ********************* 0.0 --------------------- Multilevel TTTTTTTCTTTTTTTTTTTTT consensus AC GC T CC C CC CG sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTYTTTTTYT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1542183 bayes= 11.8187 E= 3.2e-012 -70 -35 -57 72 -237 102 -133 68 -357 0 -157 116 -1761 3 51 84 -48 66 -335 52 -102 12 -188 86 -1761 -403 -198 149 -391 151 -65 28 -283 -389 -188 141 -1761 -31 19 102 -154 80 -94 61 -1761 96 -1761 102 -176 -1761 -355 140 -1761 154 -307 59 -494 -180 -134 138 -1761 1 -36 107 -1761 85 -396 105 -263 35 -38 86 -270 -153 -23 116 -349 88 21 51 -168 -65 49 74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTYTTTTTYT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2006 E= 3.2e-012 0.207876 0.127617 0.109671 0.554835 0.065304 0.330010 0.064806 0.539880 0.028415 0.163509 0.054835 0.753240 0.000000 0.166500 0.231805 0.601695 0.241775 0.257727 0.015952 0.484546 0.166500 0.176969 0.044367 0.612164 0.000000 0.009970 0.041376 0.948654 0.022433 0.463609 0.103689 0.410269 0.047358 0.010967 0.044367 0.897308 0.000000 0.131107 0.185444 0.683450 0.116152 0.284148 0.085244 0.514457 0.000000 0.316052 0.000000 0.683948 0.099202 0.000000 0.013958 0.886839 0.000000 0.474576 0.019442 0.505982 0.010967 0.046859 0.064307 0.877866 0.000000 0.164008 0.126620 0.709372 0.000000 0.293121 0.010469 0.696411 0.054337 0.207876 0.125125 0.612662 0.051844 0.056331 0.138584 0.753240 0.029910 0.300598 0.188933 0.480558 0.105184 0.104187 0.228814 0.561815 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYTTYTTTTTYT MEME-2 regular expression -------------------------------------------------------------------------------- [TA][TC]T[TG][TCA]TT[CT]TT[TC][TC]T[TC]TT[TC][TC]T[TC][TG] -------------------------------------------------------------------------------- Time 137.42 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************