******************************************************************************** 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= 2026 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= 202600 N= 2026 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.276 C 0.224 G 0.224 T 0.276 Background letter frequencies (from file dataset with add-one prior applied): A 0.276 C 0.224 G 0.224 T 0.276 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RMACGTGV MEME-1 width = 8 sites = 633 llr = 5239 E-value = 2.9e-125 ******************************************************************************** -------------------------------------------------------------------------------- Motif RMACGTGV MEME-1 Description -------------------------------------------------------------------------------- Simplified A 44a::::3 pos.-specific C 26:a:::3 probability G 4:::a:a3 matrix T :::::a:1 bits 2.2 ** * 1.9 ***** 1.7 ***** 1.5 ***** Relative 1.3 ***** Entropy 1.1 ****** (11.9 bits) 0.9 ****** 0.6 ****** 0.4 ******* 0.2 ******** 0.0 -------- Multilevel ACACGTGG consensus GA C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RMACGTGV MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 188418 bayes= 8.45284 E= 2.9e-125 60 -22 80 -1595 58 139 -1595 -1595 186 -1595 -1595 -1595 -1595 216 -1595 -1595 -1595 -1595 216 -1595 -1595 -1595 -1595 186 -1595 -1595 216 -1595 5 43 53 -164 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RMACGTGV MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 633 E= 2.9e-125 0.418641 0.192733 0.388626 0.000000 0.412322 0.587678 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.285940 0.301738 0.323855 0.088468 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RMACGTGV MEME-1 regular expression -------------------------------------------------------------------------------- [AG][CA]ACGTG[GCA] -------------------------------------------------------------------------------- Time 648.55 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************