******************************************************************************** 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 2-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/meme49 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= Noise-injected mHG starts= log likelihood ratio (LLR) strands: + - width: minw= 12 maxw= 12 nsites: minsites= 2 maxsites= 845 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= 0.5 searchsize= 16900 norand= no csites= -1 Letter frequencies in dataset: A 0.249 C 0.251 G 0.251 T 0.249 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 CRGCCMCACCCW MEME-1 width = 12 sites = 77 llr = 711 p-value = 3.4e-005 E-value = 3.4e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif CRGCCMCACCCW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 253216:7:::5 pos.-specific C 51:784a:aaa1 probability G 227::::2:::: matrix T 12:12::1:::4 bits 2.0 * * * 1.8 * *** 1.6 * *** 1.4 * *** Relative 1.2 * *** Entropy 1.0 *** *** (13.3 bits) 0.8 * ******* 0.6 ********** 0.4 ********** 0.2 ************ 0.0 ------------ Multilevel CAGCCACACCCA consensus GGA C T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRGCCMCACCCW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 9.22092 E= 3.4e-005 -45 85 -19 -80 91 -169 -3 -26 13 -269 142 -425 -56 145 -269 -126 -226 161 -1291 -45 133 58 -1291 -1291 -1291 199 -1291 -1291 152 -1291 -47 -126 -1291 199 -1291 -1291 -425 197 -1291 -1291 -1291 199 -1291 -1291 106 -95 -1291 50 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRGCCMCACCCW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 77 E= 3.4e-005 0.181818 0.454545 0.220779 0.142857 0.467532 0.077922 0.246753 0.207792 0.272727 0.038961 0.675325 0.012987 0.168831 0.688312 0.038961 0.103896 0.051948 0.766234 0.000000 0.181818 0.623377 0.376623 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.714286 0.000000 0.181818 0.103896 0.000000 1.000000 0.000000 0.000000 0.012987 0.987013 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.519481 0.129870 0.000000 0.350649 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRGCCMCACCCW MEME-1 regular expression -------------------------------------------------------------------------------- [CG][AGT][GA]CC[AC]CACCC[AT] -------------------------------------------------------------------------------- Time 1.24 secs. ******************************************************************************** ******************************************************************************** MOTIF AGRAKCTGAWAA MEME-2 width = 12 sites = 15 llr = 162 p-value = 8.0e-001 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGRAKCTGAWAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9:57::::65a7 pos.-specific C :::1:7::3::: probability G :a5152:a:1:3 matrix T 1::151a:14:: bits 2.0 * ** * 1.8 * ** * 1.6 ** ** * 1.4 ** ** * Relative 1.2 ** ** ** Entropy 1.0 *** * ** ** (15.6 bits) 0.8 *** **** *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AGGAGCTGAAAA consensus A TG CT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAKCTGAWAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 11.0366 E= 1.5e+000 191 -1055 -1055 -190 -1055 -1055 199 -1055 91 -1055 108 -1055 142 -191 -91 -90 -1055 -1055 108 91 -1055 141 -33 -90 -1055 -1055 -1055 201 -1055 -1055 199 -1055 127 8 -1055 -90 110 -1055 -191 69 201 -1055 -1055 -1055 156 -1055 8 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAKCTGAWAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 15 E= 1.5e+000 0.933333 0.000000 0.000000 0.066667 0.000000 0.000000 1.000000 0.000000 0.466667 0.000000 0.533333 0.000000 0.666667 0.066667 0.133333 0.133333 0.000000 0.000000 0.533333 0.466667 0.000000 0.666667 0.200000 0.133333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.600000 0.266667 0.000000 0.133333 0.533333 0.000000 0.066667 0.400000 1.000000 0.000000 0.000000 0.000000 0.733333 0.000000 0.266667 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAKCTGAWAA MEME-2 regular expression -------------------------------------------------------------------------------- AG[GA]A[GT][CG]TG[AC][AT]A[AG] -------------------------------------------------------------------------------- Time 2.34 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************