******************************************************************************** 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/AT3G20310_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/AT3G20310_peak_sequences.fasta -dna -oc out/AT3G20310 -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= 4588 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= 944013 N= 4588 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.257 C 0.243 G 0.243 T 0.257 Background letter frequencies (from file dataset with add-one prior applied): A 0.258 C 0.242 G 0.242 T 0.258 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YGGCGGCGGHDRHDD MEME-1 width = 15 sites = 4545 llr = 39841 E-value = 9.1e-587 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGGCGGCGGHDRHDD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 113:::::2423333 pos.-specific C 4::a::a:2311312 probability G :97:aa:85154144 matrix T 41:::::21222322 bits 2.0 *** 1.8 **** 1.6 **** 1.4 * **** Relative 1.2 * **** Entropy 1.0 * ***** (12.6 bits) 0.8 ******* 0.6 ******* 0.4 ******** 0.2 ************ * 0.0 --------------- Multilevel TGGCGGCGGAGGAGG consensus C A CAATAA sequence TT CTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGGCGGHDRHDD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 879781 bayes= 9.62368 E= 9.1e-587 -79 74 -571 78 -229 -910 185 -174 12 -387 149 -350 -1879 204 -1879 -561 -1879 -1879 205 -1879 -1879 -506 204 -1879 -357 201 -1879 -529 -407 -323 167 -46 -39 -49 109 -116 51 28 -114 -17 -9 -203 93 -12 28 -78 65 -64 28 5 -71 15 25 -113 60 -26 14 -58 54 -35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGGCGGHDRHDD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4545 E= 9.1e-587 0.149395 0.403300 0.004620 0.442684 0.052805 0.000440 0.869747 0.077008 0.280748 0.016502 0.679868 0.022882 0.000000 0.994719 0.000000 0.005281 0.000000 0.000000 1.000000 0.000000 0.000000 0.007261 0.992739 0.000000 0.021782 0.971617 0.000000 0.006601 0.015402 0.025743 0.771837 0.187019 0.196700 0.172057 0.516172 0.115072 0.367657 0.294169 0.109571 0.228603 0.241584 0.059186 0.461826 0.237404 0.314191 0.141254 0.379098 0.165457 0.313971 0.251045 0.148075 0.286909 0.307591 0.110231 0.366337 0.215842 0.284268 0.161496 0.351155 0.203080 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGCGGCGGHDRHDD MEME-1 regular expression -------------------------------------------------------------------------------- [TC]G[GA]CGGCGG[ACT][GAT][GA][ATC][GAT][GAT] -------------------------------------------------------------------------------- Time 71.32 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTTCYTCYTCYTCY MEME-2 width = 15 sites = 1320 llr = 13506 E-value = 1.3e-065 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTTCYTCYTCYTCY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:1::1::1::1::2 pos.-specific C 181173193183:84 probability G ::1:::::11:1::1 matrix T 826836916825924 bits 2.0 1.8 1.6 1.4 ** * * Relative 1.2 * * ** * ** Entropy 1.0 ** ** ** ** ** (14.8 bits) 0.8 ** ** ** ** ** 0.6 ** ***** ** ** 0.4 *********** ** 0.2 *************** 0.0 --------------- Multilevel TCTTCTTCTTCTTCT consensus TC C C TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTCYTCYTCYTCY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 879781 bayes= 11.6336 E= 1.3e-065 -214 -144 -293 167 -1701 176 -423 -62 -113 -79 -120 130 -389 -73 -300 164 -1701 161 -1701 1 -235 36 -337 125 -337 -200 -1701 183 -1701 183 -1701 -86 -216 34 -186 114 -263 -152 -225 167 -1701 176 -1701 -50 -141 45 -132 88 -299 -270 -1701 185 -1701 166 -380 -25 -70 59 -217 71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTCYTCYTCYTCY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1320 E= 1.3e-065 0.058333 0.089394 0.031818 0.820455 0.000000 0.818939 0.012879 0.168182 0.118182 0.140152 0.105303 0.636364 0.017424 0.145455 0.030303 0.806818 0.000000 0.740909 0.000000 0.259091 0.050758 0.310606 0.023485 0.615152 0.025000 0.060606 0.000000 0.914394 0.000000 0.858333 0.000000 0.141667 0.057576 0.306818 0.066667 0.568939 0.041667 0.084091 0.050758 0.823485 0.000000 0.817424 0.000000 0.182576 0.096970 0.330303 0.096970 0.475758 0.032576 0.037121 0.000000 0.930303 0.000000 0.765909 0.017424 0.216667 0.159091 0.365152 0.053788 0.421970 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTCYTCYTCYTCY MEME-2 regular expression -------------------------------------------------------------------------------- TCTT[CT][TC]TC[TC]TC[TC]T[CT][TC] -------------------------------------------------------------------------------- Time 154.81 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************