******************************************************************************** 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/meme40 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun ce -maxw 30 -searchsize 40000 -nostatus -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= Central Enrichment mBN starts= Central Enrichment binomial test strands: + - width: minw= 8 maxw= 30 nsites: minsites= 2 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 CTTATCTC MEME-1 width = 8 sites = 71 llr = 594 p-value = 5.4e-002 E-value = 5.5e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTATCTC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1::a::2: pos.-specific C 91:::a:6 probability G :::::::2 matrix T :9a:a:71 bits 2.0 * ** 1.8 **** 1.6 **** 1.4 ***** Relative 1.2 ****** Entropy 1.0 ******* (12.1 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel CTTATCTC consensus AG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTATCTC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 11.639 E= 5.5e-002 -186 181 -317 -238 -356 -116 -1217 176 -1217 -1217 -1217 196 193 -1217 -348 -1217 -1217 -1217 -1217 196 -1217 204 -1217 -1217 -10 -348 -1217 153 -1217 137 -3 -97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTATCTC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 71 E= 5.5e-002 0.070789 0.853124 0.027037 0.049050 0.021739 0.108696 0.000000 0.869565 0.000000 0.000000 0.000000 1.000000 0.978261 0.000000 0.021739 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.239130 0.021739 0.000000 0.739130 0.000000 0.630435 0.239130 0.130435 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTATCTC MEME-1 regular expression -------------------------------------------------------------------------------- CTTATC[TA][CG] -------------------------------------------------------------------------------- Time 3.45 secs. ******************************************************************************** ******************************************************************************** MOTIF GGGTGTGG MEME-2 width = 8 sites = 90 llr = 869 p-value = 2.7e-001 E-value = 3.2e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTGTGG MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1:::: pos.-specific C :::1:::1 probability G aaa:a2a8 matrix T :::9:8:2 bits 2.0 *** * * 1.8 *** * * 1.6 *** * * 1.4 ******* Relative 1.2 ******* Entropy 1.0 ******** (13.9 bits) 0.8 ******** 0.6 ******** 0.4 ******** 0.2 ******** 0.0 -------- Multilevel GGGTGTGG consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGTGG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 70185 bayes= 10.1527 E= 3.2e-001 -1234 -1234 204 -1234 -1234 -1234 204 -1234 -1234 -1234 204 -1234 -215 -208 -1234 179 -1234 -1234 204 -1234 -1234 -1234 -66 172 -1234 -1234 204 -1234 -1234 -208 166 -57 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGTGG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 90 E= 3.2e-001 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.057692 0.057692 0.000000 0.884615 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.153846 0.846154 0.000000 0.000000 1.000000 0.000000 0.000000 0.057692 0.769231 0.173077 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGTGG MEME-2 regular expression -------------------------------------------------------------------------------- GGGTGTGG -------------------------------------------------------------------------------- Time 6.72 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************