******************************************************************************** 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= 5678 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= 567797 N= 5678 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.29 C 0.21 G 0.21 T 0.29 Background letter frequencies (from file dataset with add-one prior applied): A 0.29 C 0.21 G 0.21 T 0.29 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NVRVMACGTG MEME-1 width = 10 sites = 4916 llr = 36134 E-value = 1.0e-592 ******************************************************************************** -------------------------------------------------------------------------------- Motif NVRVMACGTG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 344359:1:: pos.-specific C 22135:9::: probability G 2333:::9:a matrix T 2221:11:a: bits 2.3 * 2.0 * 1.8 **** 1.6 **** Relative 1.4 ***** Entropy 1.1 ****** (10.6 bits) 0.9 ****** 0.7 ****** 0.5 ****** 0.2 ******** 0.0 ---------- Multilevel AAAGCACGTG consensus TGGAA sequence C C G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NVRVMACGTG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 516695 bayes= 8.53129 E= 1.0e-592 7 12 12 -27 36 -12 28 -70 62 -119 37 -61 10 48 61 -195 75 129 -1891 -1891 168 -1891 -1891 -199 -1891 216 -1891 -221 -235 -1891 217 -1891 -1891 -1891 -1891 179 -1891 -1891 223 -452 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NVRVMACGTG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 4916 E= 1.0e-592 0.304312 0.228234 0.227624 0.239829 0.373271 0.192840 0.254882 0.179007 0.445891 0.092352 0.271562 0.190195 0.311229 0.293328 0.320179 0.075264 0.486574 0.513426 0.000000 0.000000 0.926770 0.000000 0.000000 0.073230 0.000000 0.937551 0.000000 0.062449 0.056753 0.000000 0.943247 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.987388 0.012612 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NVRVMACGTG MEME-1 regular expression -------------------------------------------------------------------------------- [ATCG][AG][AG][GAC][CA]ACGTG -------------------------------------------------------------------------------- Time 662.24 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (1) found. ******************************************************************************** CPU: kali.stanford.edu ********************************************************************************