******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.0 (Release date: Tue Mar 9 17:38:20 2021 -0800) 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= common/Klf1-200.fa 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 common/Klf1-200.fa -oc results/meme39 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun ce -maxw 30 -searchsize 40000 -nostatus -mpi model: mod= oops nmotifs= 2 evt= inf objective function: em= Central Enrichment mBN starts= Central Enrichment binomial test strands: + - width: minw= 8 maxw= 30 nsites: minsites= 200 maxsites= 200 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 100000 N= 200 sample: seed= 0 hsfrac= 0.5 searchsize= 40000 norand= no csites= -1 Letter frequencies in dataset: A 0.256 C 0.244 G 0.244 T 0.256 Background letter frequencies (from file dataset with add-one prior applied): A 0.256 C 0.244 G 0.244 T 0.256 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WGGGTGTG MEME-1 width = 8 sites = 200 llr = 1337 p-value = 8.4e-001 E-value = 1.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif WGGGTGTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3:::1::: pos.-specific C ::::1::: probability G 1999:929 matrix T 6:1:7:81 bits 2.0 1.8 1.6 * 1.4 *** * * Relative 1.2 *** * * Entropy 1.0 *** *** (9.6 bits) 0.8 ******* 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel TGGGTGTG consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGGTGTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 9.49399 E= 1.6e+000 42 -384 -149 111 -327 -410 194 -327 -410 -410 190 -206 -236 -270 188 -410 -100 -139 -282 154 -245 -240 188 -442 -344 -442 -30 158 -344 -341 188 -213 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGGTGTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 200 E= 1.6e+000 0.343462 0.017003 0.086771 0.552764 0.026528 0.014169 0.932774 0.026528 0.014901 0.014169 0.909518 0.061412 0.049784 0.037425 0.897890 0.014901 0.128200 0.092731 0.034591 0.744479 0.046804 0.046219 0.895056 0.011920 0.023548 0.011335 0.197382 0.767734 0.023548 0.022963 0.895056 0.058432 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGGTGTG MEME-1 regular expression -------------------------------------------------------------------------------- [TA]GGGTGTG -------------------------------------------------------------------------------- Time 2.61 secs. ******************************************************************************** ******************************************************************************** MOTIF RGRGARRG MEME-2 width = 8 sites = 200 llr = 1035 p-value = 9.8e-001 E-value = 3.0e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGRGARRG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 51517441 pos.-specific C :1:::::: probability G 49582568 matrix T :::::::: bits 2.0 1.8 1.6 1.4 Relative 1.2 * * * Entropy 1.0 * ** * (7.5 bits) 0.8 ***** * 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel AGGGAGGG consensus G A GAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGRGARRG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 9.58604 E= 3.0e+000 108 -348 70 -265 -183 -220 181 -380 86 -380 104 -380 -103 -380 178 -380 154 -422 -22 -302 68 -380 113 -282 57 -348 119 -265 -98 -348 176 -348 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGRGARRG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 200 E= 3.0e+000 0.540740 0.021760 0.396760 0.040740 0.071878 0.053122 0.856694 0.018306 0.464735 0.017408 0.499551 0.018306 0.125449 0.017408 0.838836 0.018306 0.745873 0.013056 0.209484 0.031587 0.411164 0.017408 0.535265 0.036164 0.380026 0.021760 0.557474 0.040740 0.130026 0.021760 0.825331 0.022883 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGRGARRG MEME-2 regular expression -------------------------------------------------------------------------------- [AG]G[GA]G[AG][GA][GA]G -------------------------------------------------------------------------------- Time 5.01 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************