******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.0.1 (Release date: Thu Jul 26 17:15:19 2018 -0700) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme-suite.org . This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://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= 100_around_summits.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 100_around_summits.fa -dna -revcomp -o meme_out model: mod= zoops nmotifs= 1 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 8 maxw= 50 nsites: minsites= 2 maxsites= 1223 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= 122300 N= 1223 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.289 C 0.211 G 0.211 T 0.289 Background letter frequencies (from file dataset with add-one prior applied): A 0.289 C 0.211 G 0.211 T 0.289 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF KCACGTGAYNWNM MEME-1 width = 13 sites = 318 llr = 3019 E-value = 7.6e-205 ******************************************************************************** -------------------------------------------------------------------------------- Motif KCACGTGAYNWNM MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:a::::8:2434 pos.-specific C 2a:9:::243223 probability G 4:::a:a::2132 matrix T 3::1:a::53432 bits 2.2 * * 2.0 * * * 1.8 ** *** 1.6 ****** Relative 1.3 ****** Entropy 1.1 ****** (13.7 bits) 0.9 ******* 0.7 ******** 0.4 ******** 0.2 ********* 0.0 ------------- Multilevel GCACGTGATCAAA consensus T CCTTGC sequence A T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACGTGAYNWNM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 107624 bayes= 9.33837 E= 7.6e-205 -85 -45 83 11 -282 219 -1496 -1496 179 -1496 -1496 -1496 -1496 207 -1496 -131 -1496 -1496 225 -1496 -1496 -1496 -1496 179 -1496 -1496 225 -1496 138 0 -506 -335 -262 98 -448 87 -30 50 -18 -5 30 -45 -64 30 3 -34 41 -17 38 52 -48 -77 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACGTGAYNWNM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 318 E= 7.6e-205 0.160377 0.154088 0.374214 0.311321 0.040881 0.959119 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.883648 0.000000 0.116352 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.754717 0.210692 0.006289 0.028302 0.047170 0.415094 0.009434 0.528302 0.235849 0.298742 0.185535 0.279874 0.355346 0.154088 0.135220 0.355346 0.295597 0.166667 0.279874 0.257862 0.377358 0.301887 0.150943 0.169811 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCACGTGAYNWNM MEME-1 regular expression -------------------------------------------------------------------------------- [GT]CACGTG[AC][TC][CTA][AT][AGT][AC] -------------------------------------------------------------------------------- Time 633.41 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************