******************************************************************************** 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/AT1G28160_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/AT1G28160_peak_sequences.fasta -dna -oc out/AT1G28160 -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= 2180 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= 507388 N= 2180 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.244 C 0.256 G 0.256 T 0.244 Background letter frequencies (from file dataset with add-one prior applied): A 0.244 C 0.256 G 0.256 T 0.244 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YDYCKCCGCCGYCRH MEME-1 width = 15 sites = 2146 llr = 19716 E-value = 6.5e-572 ******************************************************************************** -------------------------------------------------------------------------------- Motif YDYCKCCGCCGYCRH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 23112:::::::242 pos.-specific C 4157:8a:aa:56:4 probability G 121:41:a::a1:41 matrix T 343141:::::4222 bits 2.0 ** 1.8 * *** 1.6 ***** 1.4 ***** Relative 1.2 ***** Entropy 1.0 ***** (13.3 bits) 0.8 * ****** 0.6 * ****** 0.4 ********** 0.2 *************** 0.0 --------------- Multilevel CTCCGCCGCCGCCAC consensus TAT T T GA sequence AG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YDYCKCCGCCGYCRH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 476868 bayes= 9.55297 E= 6.5e-572 -20 80 -195 17 18 -114 -5 56 -118 88 -152 44 -135 154 -280 -97 -58 -348 71 70 -348 155 -136 -93 -408 195 -1771 -903 -387 -1771 191 -361 -1771 192 -358 -471 -1771 196 -1771 -645 -1771 -1771 197 -1771 -285 100 -157 59 -50 123 -248 -42 65 -244 57 -37 0 71 -119 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YDYCKCCGCCGYCRH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2146 E= 6.5e-572 0.212954 0.445480 0.066170 0.275396 0.277726 0.115564 0.247437 0.359273 0.107642 0.471575 0.089003 0.331780 0.095993 0.742777 0.036813 0.124418 0.163560 0.022833 0.417055 0.396552 0.021901 0.750699 0.099254 0.128145 0.014445 0.985089 0.000000 0.000466 0.016775 0.000000 0.963187 0.020037 0.000000 0.969245 0.021435 0.009320 0.000000 0.997204 0.000000 0.002796 0.000000 0.000000 1.000000 0.000000 0.034017 0.510718 0.086207 0.369059 0.172414 0.599720 0.045666 0.182199 0.383970 0.047064 0.379310 0.189655 0.243709 0.417055 0.112302 0.226934 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YDYCKCCGCCGYCRH MEME-1 regular expression -------------------------------------------------------------------------------- [CTA][TAG][CT]C[GT]CCGCCG[CT]C[AG][CAT] -------------------------------------------------------------------------------- Time 119.87 secs. ******************************************************************************** ******************************************************************************** MOTIF CTYCTYCTYYTYCTY MEME-2 width = 15 sites = 1061 llr = 9928 E-value = 7.6e-136 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTYCTYCTYYTYCTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:::1::1::1::11 pos.-specific C 6:5724a:6624816 probability G :1::1::1::1::11 matrix T 385366:84465273 bits 2.0 1.8 1.6 * 1.4 * Relative 1.2 * * Entropy 1.0 * * *** * * (13.5 bits) 0.8 *** ***** ** 0.6 ********** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CTCCTTCTCCTTCTC consensus T TT C TT CT T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYCTYCTYYTYCTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 476868 bayes= 11.0904 E= 7.6e-136 -124 121 -399 25 -1670 -369 -78 177 -1670 102 -408 94 -1670 143 -1670 35 -102 -51 -200 138 -802 72 -808 124 -393 191 -328 -1670 -115 -1670 -111 166 -1670 128 -344 54 -1670 120 -438 72 -138 -57 -78 126 -1670 81 -391 113 -350 160 -1670 -28 -86 -124 -167 147 -219 111 -230 48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYCTYCTYYTYCTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1061 E= 7.6e-136 0.103676 0.589067 0.016023 0.291235 0.000000 0.019793 0.148916 0.831291 0.000000 0.517436 0.015080 0.467484 0.000000 0.688973 0.000000 0.311027 0.120641 0.180019 0.064090 0.635250 0.000943 0.421301 0.000943 0.576814 0.016023 0.957587 0.026390 0.000000 0.110273 0.000000 0.118756 0.770971 0.000000 0.620170 0.023563 0.356268 0.000000 0.585297 0.012253 0.402451 0.094251 0.172479 0.148916 0.584354 0.000000 0.447691 0.016965 0.535344 0.021678 0.776626 0.000000 0.201697 0.134779 0.108388 0.080113 0.676720 0.053723 0.553252 0.051838 0.341188 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYCTYCTYYTYCTY MEME-2 regular expression -------------------------------------------------------------------------------- [CT]T[CT][CT]T[TC]CT[CT][CT]T[TC][CT]T[CT] -------------------------------------------------------------------------------- Time 227.92 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************