******************************************************************************** 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/AT5G17300_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/AT5G17300_peak_sequences.fasta -dna -oc out/AT5G17300 -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= 9702 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= 2387295 N= 9702 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.372 C 0.128 G 0.128 T 0.372 Background letter frequencies (from file dataset with add-one prior applied): A 0.373 C 0.127 G 0.127 T 0.373 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAAAAATATCT MEME-1 width = 11 sites = 9665 llr = 70650 E-value = 1.9e-214 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAAAAATATCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4569aa3a::2 pos.-specific C 211::::::a1 probability G 121:::::::: matrix T 3221::7:a:7 bits 3.0 * 2.7 * 2.4 * 2.1 * Relative 1.8 * Entropy 1.5 * *** (10.5 bits) 1.2 ** *** 0.9 *** *** 0.6 ******* 0.3 ********** 0.0 ----------- Multilevel AAAAAATATCT consensus T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAAAATATCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2290275 bayes= 9.97782 E= 1.9e-214 18 55 6 -52 54 10 31 -117 77 -59 -64 -93 126 -468 -339 -202 141 -526 -1988 -612 139 -459 -356 -551 -52 -1988 -285 95 142 -1026 -1988 -1988 -1988 -1988 -1988 142 -882 297 -1988 -571 -116 -13 -435 93 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAAAATATCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 9665 E= 1.9e-214 0.421314 0.186342 0.132023 0.260321 0.540921 0.135541 0.157786 0.165753 0.638386 0.084428 0.081531 0.195654 0.891154 0.004966 0.012106 0.091774 0.991309 0.003311 0.000000 0.005380 0.975789 0.005277 0.010760 0.008174 0.260735 0.000000 0.017589 0.721676 0.999897 0.000103 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000828 0.992033 0.000000 0.007139 0.167408 0.115882 0.006208 0.710502 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAAAAATATCT MEME-1 regular expression -------------------------------------------------------------------------------- [AT]AAAAA[TA]ATCT -------------------------------------------------------------------------------- Time 69.86 secs. ******************************************************************************** ******************************************************************************** MOTIF GCGGTRTACCGCGGG MEME-2 width = 15 sites = 89 llr = 1697 E-value = 1.7e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCGGTRTACCGCGGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :22116:8::::31: pos.-specific C :82:1:::78:9::: probability G a:6924:::2a:79a matrix T ::::7:923:::::: bits 3.0 * * 2.7 * ** * 2.4 * * ** ** 2.1 * * *** ** Relative 1.8 ** * *** ** Entropy 1.5 ** * ******* (27.5 bits) 1.2 **** ******* 0.9 **** ** ******* 0.6 *************** 0.3 *************** 0.0 --------------- Multilevel GCGGTATACCGCGGG consensus A G TTG A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGTRTACCGCGGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2251467 bayes= 16.7101 E= 1.7e-005 -1312 -191 293 -1312 -81 261 -1312 -505 -125 59 231 -405 -247 -350 286 -1312 -247 -118 50 90 65 -350 167 -1312 -305 -1312 -191 130 103 -1312 -1312 -66 -505 243 -350 -35 -1312 263 75 -1312 -1312 -1312 298 -1312 -1312 289 -350 -305 -25 -1312 243 -1312 -205 -1312 284 -1312 -505 -1312 296 -1312 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGTRTACCGCGGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 89 E= 1.7e-005 0.000000 0.033708 0.966292 0.000000 0.213483 0.775281 0.000000 0.011236 0.157303 0.191011 0.629213 0.022472 0.067416 0.011236 0.921348 0.000000 0.067416 0.056180 0.179775 0.696629 0.584270 0.011236 0.404494 0.000000 0.044944 0.000000 0.033708 0.921348 0.764045 0.000000 0.000000 0.235955 0.011236 0.685393 0.011236 0.292135 0.000000 0.786517 0.213483 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.943820 0.011236 0.044944 0.314607 0.000000 0.685393 0.000000 0.089888 0.000000 0.910112 0.000000 0.011236 0.000000 0.988764 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCGGTRTACCGCGGG MEME-2 regular expression -------------------------------------------------------------------------------- G[CA]GGT[AG]T[AT][CT][CG]GC[GA]GG -------------------------------------------------------------------------------- Time 133.24 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************