******************************************************************************** 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/Klf1-200-100.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 -csites 30 common/Klf1-200-100.fa -oc results/meme7 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= oops nmotifs= 2 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= 169 maxsites= 169 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= 16900 N= 169 sample: seed= 0 hsfrac= 0 searchsize= 16900 norand= no csites= 30 Letter frequencies in dataset: A 0.248 C 0.252 G 0.252 T 0.248 Background letter frequencies (from file dataset with add-one prior applied): A 0.248 C 0.252 G 0.252 T 0.248 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF VAGMRRCMAGR MEME-1 width = 11 sites = 169 llr = 772 E-value = 3.2e+013 ******************************************************************************** -------------------------------------------------------------------------------- Motif VAGMRRCMAGR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 48154415925 pos.-specific C 3:131:63:12 probability G 3:72352:173 matrix T :21:2112::: bits 2.0 1.8 1.6 1.4 * Relative 1.2 * Entropy 1.0 * * (6.6 bits) 0.8 ** ** 0.6 ** * ** 0.4 *** ****** 0.2 *********** 0.0 ----------- Multilevel AAGAAGCAAGA consensus C CGAGC G sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VAGMRRCMAGR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 13237 bayes= 7.83298 E= 3.2e+013 56 29 15 -239 165 -340 -260 -69 -135 -112 155 -231 110 15 -54 -423 76 -150 42 -69 59 -260 98 -149 -141 130 -13 -211 87 42 -341 -44 182 -508 -192 -235 -52 -220 155 -275 95 -12 11 -381 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VAGMRRCMAGR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 169 E= 3.2e+013 0.366790 0.307766 0.278180 0.047264 0.780991 0.023742 0.041494 0.153772 0.097578 0.115440 0.736742 0.050241 0.533978 0.279632 0.173123 0.013268 0.420081 0.088794 0.337315 0.153809 0.372744 0.041457 0.497078 0.088721 0.093168 0.619850 0.229318 0.057665 0.455584 0.337315 0.023705 0.183395 0.877173 0.007443 0.066614 0.048770 0.173031 0.054780 0.735253 0.036936 0.479253 0.230806 0.272226 0.017715 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif VAGMRRCMAGR MEME-1 regular expression -------------------------------------------------------------------------------- [ACG]AG[AC][AG][GA][CG][AC]AG[AGC] -------------------------------------------------------------------------------- Time 0.47 secs. ******************************************************************************** ******************************************************************************** MOTIF MCACCCWG MEME-2 width = 8 sites = 169 llr = 757 E-value = 8.7e+023 ******************************************************************************** -------------------------------------------------------------------------------- Motif MCACCCWG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 618:2162 pos.-specific C 38:87911 probability G ::11:::5 matrix T 1:111:42 bits 2.0 1.8 1.6 1.4 Relative 1.2 * * Entropy 1.0 * * * (6.5 bits) 0.8 *** * 0.6 ******* 0.4 ******* 0.2 ******** 0.0 -------- Multilevel ACACCCAG consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACCCWG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 13744 bayes= 7.88744 E= 8.7e+023 123 39 -350 -197 -154 175 -323 -249 162 -271 -92 -200 -264 174 -212 -197 -71 142 -288 -82 -169 176 -282 -281 115 -208 -340 56 -39 -109 102 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACCCWG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 169 E= 8.7e+023 0.584255 0.329946 0.022254 0.063545 0.085707 0.843287 0.026719 0.044287 0.766180 0.038554 0.133228 0.062038 0.039839 0.838859 0.057794 0.063508 0.152266 0.673178 0.034125 0.140431 0.076813 0.852182 0.035614 0.035392 0.550185 0.059282 0.023779 0.366753 0.189239 0.118454 0.508986 0.183321 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCACCCWG MEME-2 regular expression -------------------------------------------------------------------------------- [AC]CACCC[AT]G -------------------------------------------------------------------------------- Time 0.86 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local 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