******************************************************************************** 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/AT4G21080_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/AT4G21080_peak_sequences.fasta -dna -oc out/AT4G21080 -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= 6729 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= 1529648 N= 6729 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.36 C 0.14 G 0.14 T 0.36 Background letter frequencies (from file dataset with add-one prior applied): A 0.36 C 0.14 G 0.14 T 0.36 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTTTTTTTTTTTTTTTTTTTT MEME-1 width = 21 sites = 6707 llr = 48493 E-value = 2.6e-207 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTTTTTTTTTTTTTTTTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:::11111111111212122 pos.-specific C 8:1111212212212222212 probability G 1::::1211111111111111 matrix T :a9988566777776566565 bits 2.8 2.6 2.3 2.0 * Relative 1.7 * Entropy 1.4 * (10.4 bits) 1.1 **** 0.9 **** 0.6 ****** * * 0.3 ******************** 0.0 --------------------- Multilevel CTTTTTTTTTTTTTTTTTTTT consensus C C C C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTTTTTTTTTTTTTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1395068 bayes= 9.68581 E= 2.6e-207 -256 259 -95 -381 -437 -295 -587 142 -765 -86 -728 135 -1936 -68 -511 133 -129 -141 -250 111 -225 -33 -117 106 -158 77 12 45 -130 2 -17 71 -166 50 -39 69 -174 20 -89 87 -197 4 -144 98 -184 16 -115 92 -231 42 -92 89 -158 -23 -42 86 -166 43 -54 74 -107 67 -124 60 -155 15 -26 75 -99 16 -56 65 -127 56 -38 58 -107 10 -15 61 -76 63 -48 39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTTTTTTTTTTTTTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6707 E= 2.6e-207 0.061130 0.841211 0.072014 0.025645 0.017444 0.018041 0.002386 0.962129 0.001789 0.077084 0.000895 0.920233 0.000000 0.086924 0.004026 0.909050 0.147309 0.052632 0.024601 0.775458 0.075891 0.110780 0.061876 0.751454 0.120471 0.237364 0.151334 0.490830 0.146414 0.141494 0.123900 0.588191 0.114060 0.197406 0.106605 0.581929 0.107947 0.159982 0.075294 0.656777 0.091993 0.143134 0.051439 0.713434 0.100492 0.156255 0.062770 0.680483 0.072909 0.186522 0.073654 0.666915 0.120173 0.119278 0.104369 0.656180 0.114358 0.188013 0.096019 0.601610 0.171463 0.222156 0.059043 0.547339 0.123155 0.154913 0.116893 0.605040 0.181750 0.156255 0.094826 0.567169 0.149098 0.206352 0.107052 0.537498 0.172208 0.149545 0.126137 0.552110 0.212465 0.215894 0.100343 0.471299 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTTTTTTTTTTTTTTTTTTT MEME-1 regular expression -------------------------------------------------------------------------------- CTTTTT[TC]TTTTTTTT[TC]TT[TC]T[TCA] -------------------------------------------------------------------------------- Time 82.78 secs. ******************************************************************************** ******************************************************************************** MOTIF NAAAAAGT MEME-2 width = 8 sites = 6713 llr = 40893 E-value = 7.6e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif NAAAAAGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 488aaa:1 pos.-specific C 2::::::1 probability G 31::::a2 matrix T 2:2::::6 bits 2.8 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (8.8 bits) 1.1 **** 0.9 * **** 0.6 ****** 0.3 ******* 0.0 -------- Multilevel AAAAAAGT consensus G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1482545 bayes= 9.77263 E= 7.6e-010 3 44 85 -92 122 -223 -74 -291 111 -380 -168 -110 147 -1936 -987 -1936 145 -1936 -348 -1936 147 -1936 -1936 -1124 -472 -887 282 -1124 -186 -15 49 68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 6713 E= 7.6e-010 0.369283 0.188887 0.251601 0.190228 0.838522 0.029793 0.083718 0.047967 0.778638 0.009981 0.043647 0.167734 0.999851 0.000000 0.000149 0.000000 0.987487 0.000000 0.012513 0.000000 0.999851 0.000000 0.000000 0.000149 0.013705 0.000298 0.985848 0.000149 0.099508 0.125428 0.196484 0.578579 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NAAAAAGT MEME-2 regular expression -------------------------------------------------------------------------------- [AG]AAAAAGT -------------------------------------------------------------------------------- Time 153.15 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************