******************************************************************************** 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= 1061 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= 106098 N= 1061 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.294 C 0.206 G 0.206 T 0.294 Background letter frequencies (from file dataset with add-one prior applied): A 0.294 C 0.206 G 0.206 T 0.294 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WKCACGTGAYH MEME-1 width = 11 sites = 539 llr = 5348 E-value = 1.1e-689 ******************************************************************************** -------------------------------------------------------------------------------- Motif WKCACGTGAYH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 41:a:1::9:2 pos.-specific C 21a:9:::164 probability G 23:::9:a::1 matrix T 24::1:a::43 bits 2.3 * * 2.1 * * 1.8 *** ** 1.6 ****** Relative 1.4 ******* Entropy 1.1 ******* (14.3 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ********** 0.0 ----------- Multilevel ATCACGTGACC consensus TG TT sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WKCACGTGAYH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 95488 bayes= 9.4814 E= 1.1e-689 58 -44 -35 -25 -108 -55 67 42 -1572 228 -1572 -1572 177 -1572 -1572 -1572 -1572 216 -362 -222 -206 -289 213 -1572 -1572 -1572 -1572 177 -1572 -1572 228 -1572 163 -124 -1572 -1572 -385 144 -1572 52 -45 101 -109 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WKCACGTGAYH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 539 E= 1.1e-689 0.439703 0.152134 0.161410 0.246753 0.139147 0.141002 0.326531 0.393321 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.920223 0.016698 0.063080 0.070501 0.027829 0.901670 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.912801 0.087199 0.000000 0.000000 0.020408 0.558442 0.000000 0.421150 0.215213 0.415584 0.096475 0.272727 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WKCACGTGAYH MEME-1 regular expression -------------------------------------------------------------------------------- [AT][TG]CACGTGA[CT][CTA] -------------------------------------------------------------------------------- Time 632.10 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************