******************************************************************************** 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= Primary sequences shuffled preserving 3-mers 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/Klf1-200-100.fa -oc results/meme25 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus -mpi model: mod= oops nmotifs= 2 evt= inf objective function: em= Differential Enrichment mHG starts= log likelihood ratio (LLR) strands: + - width: minw= 12 maxw= 12 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 data: n= 16900 N= 169 sample: seed= 0 hsfrac= 0.6 searchsize= 16900 norand= no csites= -1 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 TSTGTCTGYYMY MEME-1 width = 12 sites = 169 llr = 808 p-value = 2.0e-001 E-value = 2.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif TSTGTCTGYYMY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:11:11:1131 pos.-specific C 15:227:23455 probability G 23:621:6211: matrix T 519261915413 bits 2.0 1.8 1.6 1.4 Relative 1.2 * * Entropy 1.0 * * (6.9 bits) 0.8 * ** 0.6 * **** 0.4 ******** * 0.2 ************ 0.0 ------------ Multilevel TCTGTCTGTTCC consensus G C CCCAT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTGTCTGYYMY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 6.25409 E= 2.0e-001 -46 -120 -58 112 -287 111 26 -102 -184 -350 -288 181 -197 -72 124 -40 -423 -27 -54 128 -187 157 -128 -164 -118 -360 -481 179 -264 -10 129 -116 -231 16 -48 97 -178 55 -87 76 36 89 -174 -82 -76 91 -265 46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTGTCTGYYMY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 2.0e-001 0.180418 0.109523 0.168694 0.541365 0.033959 0.542964 0.300360 0.122717 0.069462 0.022254 0.034088 0.874196 0.063545 0.152431 0.596218 0.187805 0.013268 0.208626 0.173123 0.604984 0.067992 0.748576 0.103606 0.079826 0.109412 0.020765 0.008931 0.860891 0.039876 0.235272 0.613970 0.110882 0.050241 0.281120 0.180529 0.488110 0.072439 0.368389 0.137620 0.421552 0.317983 0.466041 0.075508 0.140468 0.146385 0.471958 0.040005 0.341651 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TSTGTCTGYYMY MEME-1 regular expression -------------------------------------------------------------------------------- T[CG]TG[TC]CT[GC][TC][TC][CA][CT] -------------------------------------------------------------------------------- Time 0.34 secs. ******************************************************************************** ******************************************************************************** MOTIF CCASCYYYTYCH MEME-2 width = 12 sites = 169 llr = 664 p-value = 9.6e-001 E-value = 9.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCASCYYYTYCH MEME-2 Description -------------------------------------------------------------------------------- Simplified A 117111111113 pos.-specific C 781474542562 probability G 1::41:111211 matrix T 112115346324 bits 2.0 1.8 1.6 1.4 Relative 1.2 Entropy 1.0 * (5.7 bits) 0.8 *** 0.6 *** * * 0.4 *** *** * * 0.2 ************ 0.0 ------------ Multilevel CCAGCTCCTCCT consensus TC CTTCTTA sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCASCYYYTYCH MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 6.25409 E= 9.6e-001 -164 154 -216 -90 -124 165 -350 -161 144 -198 -316 -8 -193 59 72 -81 -93 145 -171 -122 -79 53 -276 88 -113 104 -148 17 -79 68 -148 54 -120 -19 -122 118 -178 90 -35 8 -159 132 -208 -11 36 -17 -228 71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCASCYYYTYCH MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 9.6e-001 0.079790 0.730861 0.056305 0.133044 0.104928 0.791521 0.022291 0.081260 0.672976 0.063711 0.028208 0.235106 0.064978 0.378809 0.414312 0.141901 0.130067 0.686501 0.077034 0.106398 0.143371 0.362546 0.037102 0.456981 0.113786 0.516392 0.090356 0.279466 0.143371 0.403966 0.090356 0.362306 0.107868 0.220534 0.108108 0.563490 0.072365 0.469055 0.196865 0.261715 0.082730 0.627330 0.059282 0.230659 0.317946 0.223474 0.051877 0.406703 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCASCYYYTYCH MEME-2 regular expression -------------------------------------------------------------------------------- CC[AT][GC]C[TC][CT][CT][TC][CT][CT][TAC] -------------------------------------------------------------------------------- Time 0.62 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************