******************************************************************************** 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/AT3G15210_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/AT3G15210_peak_sequences.fasta -dna -oc out/AT3G15210 -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= 7487 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= 1660814 N= 7487 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.264 C 0.236 G 0.236 T 0.264 Background letter frequencies (from file dataset with add-one prior applied): A 0.265 C 0.235 G 0.235 T 0.265 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HDDYGGCGGCGRHDD MEME-1 width = 15 sites = 7460 llr = 60886 E-value = 9.3e-388 ******************************************************************************** -------------------------------------------------------------------------------- Motif HDDYGGCGGCGRHDD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4441:3:::1:3433 pos.-specific C 2115::a::9:1211 probability G 123:86:aa:84143 matrix T 33341:::::21322 bits 2.1 * 1.9 *** 1.7 *** 1.5 **** Relative 1.3 * **** Entropy 1.0 * ***** (11.8 bits) 0.8 * ***** 0.6 ******** 0.4 ******** 0.2 *********** * 0.0 --------------- Multilevel AAACGGCGGCGGAGG consensus TTGT A ATAA sequence CGT CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDYGGCGGCGRHDD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1555996 bayes= 9.73103 E= 9.3e-388 42 0 -111 19 52 -132 1 13 58 -150 21 -8 -93 99 -1951 57 -241 -687 184 -133 8 -228 142 -264 -1951 208 -1951 -642 -1094 -1951 205 -359 -509 -291 202 -642 -197 192 -1951 -270 -305 -393 171 -53 15 -84 88 -92 52 1 -98 -1 5 -192 89 -23 33 -91 55 -42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDYGGCGGCGRHDD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7460 E= 9.3e-388 0.353083 0.234853 0.109383 0.302681 0.379491 0.094638 0.237399 0.288472 0.394772 0.083244 0.271850 0.250134 0.139142 0.469303 0.000000 0.391555 0.049732 0.002011 0.843029 0.105228 0.279491 0.048391 0.629625 0.042493 0.000000 0.996917 0.000000 0.003083 0.000134 0.000000 0.977882 0.021984 0.007775 0.031233 0.957909 0.003083 0.067560 0.891823 0.000000 0.040617 0.032038 0.015416 0.769705 0.182842 0.293700 0.131769 0.434853 0.139678 0.380563 0.237802 0.119705 0.261930 0.274665 0.062198 0.436863 0.226273 0.332038 0.125603 0.344102 0.198257 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDDYGGCGGCGRHDD MEME-1 regular expression -------------------------------------------------------------------------------- [ATC][ATG][AGT][CT]G[GA]CGGCG[GA][ATC][GAT][GA] -------------------------------------------------------------------------------- Time 70.44 secs. ******************************************************************************** ******************************************************************************** MOTIF YTCYTYYTCYTYYTC MEME-2 width = 15 sites = 2642 llr = 25924 E-value = 2.0e-098 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTCYTYYTCYTYYTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21:11:::::::11: pos.-specific C 4174264:84266:7 probability G :1::1::::11:::: matrix T 4836745a2584493 bits 2.1 1.9 1.7 * 1.5 ** * Relative 1.3 ** ** Entropy 1.0 * * ** ** (14.2 bits) 0.8 ** **** ***** 0.6 ************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CTCTTCTTCTTCCTC consensus T TC TC C TT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCYTYYTCYTYYTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1555996 bayes= 11.5061 E= 2.0e-098 -64 89 -1801 58 -205 -126 -164 153 -375 160 -1801 2 -199 58 -301 106 -223 -47 -190 142 -413 142 -1801 42 -248 90 -1801 96 -786 -324 -1801 188 -1801 180 -1801 -57 -279 71 -214 98 -314 -57 -198 151 -445 135 -315 46 -220 133 -1801 41 -202 -511 -403 179 -1801 167 -828 -8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCYTYYTCYTYYTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2642 E= 2.0e-098 0.169190 0.435655 0.000000 0.395155 0.063967 0.098410 0.075322 0.762301 0.019682 0.712339 0.000000 0.267979 0.066616 0.350871 0.029145 0.553369 0.056397 0.170326 0.063210 0.710068 0.015140 0.630204 0.000000 0.354656 0.047313 0.439818 0.000000 0.512869 0.001136 0.024981 0.000000 0.973883 0.000000 0.821726 0.000000 0.178274 0.038229 0.385693 0.053369 0.522710 0.029902 0.158970 0.059803 0.751325 0.012112 0.598410 0.026495 0.362983 0.057532 0.591597 0.000000 0.350871 0.065102 0.006813 0.014383 0.913702 0.000000 0.748675 0.000757 0.250568 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTCYTYYTCYTYYTC MEME-2 regular expression -------------------------------------------------------------------------------- [CT]T[CT][TC]T[CT][TC]TC[TC]T[CT][CT]T[CT] -------------------------------------------------------------------------------- Time 138.82 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************