******************************************************************************** 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/AT2G44940_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/AT2G44940_peak_sequences.fasta -dna -oc out/AT2G44940 -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= 5461 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= 1225989 N= 5461 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.293 C 0.207 G 0.207 T 0.293 Background letter frequencies (from file dataset with add-one prior applied): A 0.296 C 0.204 G 0.204 T 0.296 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDTGTCGGYG MEME-1 width = 10 sites = 5435 llr = 47059 E-value = 1.8e-486 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDTGTCGGYG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 321::::::2 pos.-specific C 113::a::31 probability G 22:a::aa:5 matrix T 446:9:::62 bits 2.3 * *** 2.1 * *** 1.8 * *** 1.6 * *** Relative 1.4 ***** Entropy 1.1 ***** (12.5 bits) 0.9 ****** 0.7 ******* 0.5 ******* 0.2 ******** 0.0 ---------- Multilevel TTTGTCGGTG consensus AGC CT sequence GA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDTGTCGGYG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 1176840 bayes= 9.94901 E= 1.8e-486 -9 -55 9 30 -34 -54 21 40 -214 45 -312 109 -1905 -1905 229 -1065 -330 -1905 -297 167 -1065 229 -1905 -1905 -1905 -1905 229 -1905 -719 -1905 229 -706 -765 77 -1905 113 -62 -90 128 -54 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDTGTCGGYG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 5435 E= 1.8e-486 0.278565 0.140018 0.216743 0.364673 0.233119 0.140386 0.236615 0.389880 0.067157 0.279301 0.023551 0.629991 0.000000 0.000000 0.999816 0.000184 0.029991 0.000000 0.026127 0.943882 0.000184 0.999816 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.002024 0.000000 0.995768 0.002208 0.001472 0.349586 0.000000 0.648942 0.192272 0.109844 0.494940 0.202944 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDTGTCGGYG MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][TGA][TC]GTCGG[TC][GT] -------------------------------------------------------------------------------- Time 119.41 secs. ******************************************************************************** ******************************************************************************** MOTIF DYCDYCDYCKYCDYCDYCRY MEME-2 width = 20 sites = 1069 llr = 12016 E-value = 2.0e-082 ******************************************************************************** -------------------------------------------------------------------------------- Motif DYCDYCDYCKYCDYCDYCRY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3113::41:2113::3113: pos.-specific C 259:6816a:57:59:69:5 probability G 2::3::3::51:41:4::52 matrix T 34143133:33144133123 bits 2.3 2.1 * 1.8 * 1.6 * * * Relative 1.4 * * * * * Entropy 1.1 * * * * * (16.2 bits) 0.9 * ** * * * * 0.7 ** ** ** * ** ** 0.5 ***** ************* 0.2 ******************* 0.0 -------------------- Multilevel TCCTCCACCGCCGCCGCCGC consensus AT AT GT TT TT TT AT sequence G T A A A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYCDYCDYCKYCDYCDYCRY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1122230 bayes= 12.3361 E= 2.0e-082 8 -42 -12 23 -181 130 -1671 49 -233 211 -1671 -237 5 -1671 42 51 -730 158 -234 23 -309 205 -1671 -134 26 -184 66 -15 -165 152 -1671 11 -360 225 -1671 -830 -48 -1671 115 18 -206 139 -128 6 -133 180 -238 -114 -20 -1671 87 31 -830 138 -117 34 -422 214 -431 -198 -17 -1671 105 9 -235 151 -260 13 -213 208 -445 -233 -17 -256 120 -34 -313 126 -31 8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYCDYCDYCKYCDYCDYCRY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1069 E= 2.0e-082 0.311506 0.152479 0.188026 0.347989 0.084191 0.501403 0.000000 0.414406 0.058934 0.884004 0.000000 0.057063 0.305893 0.000000 0.273152 0.420954 0.001871 0.610851 0.040225 0.347053 0.034612 0.848457 0.000000 0.116932 0.353601 0.057063 0.322732 0.266604 0.094481 0.586529 0.000000 0.318990 0.024322 0.974743 0.000000 0.000935 0.211413 0.000000 0.452760 0.335828 0.071094 0.536950 0.084191 0.307764 0.117867 0.709074 0.039289 0.133770 0.258185 0.000000 0.374181 0.367633 0.000935 0.533209 0.090739 0.375117 0.015903 0.898971 0.010290 0.074836 0.261927 0.000000 0.423761 0.314312 0.057998 0.583723 0.033676 0.324602 0.067353 0.864359 0.009355 0.058934 0.261927 0.034612 0.470533 0.232928 0.033676 0.488307 0.164640 0.313377 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYCDYCDYCKYCDYCDYCRY MEME-2 regular expression -------------------------------------------------------------------------------- [TA][CT]C[TAG][CT]C[AGT][CT]C[GTA][CT]C[GTA][CT]C[GTA][CT]C[GAT][CT] -------------------------------------------------------------------------------- Time 227.65 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************