******************************************************************************** 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/meme27 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= Differential Enrichment 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= 0.6 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 GGGTGKGGYMRG MEME-1 width = 12 sites = 50 llr = 435 p-value = 2.6e-002 E-value = 2.6e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTGKGGYMRG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1::3:111:43: pos.-specific C ::11::::53:1 probability G 8a9:a4892258 matrix T :::6:51:312: bits 2.0 * * 1.8 * * 1.6 * * 1.4 ** * * Relative 1.2 *** * ** * Entropy 1.0 *** * ** * (12.6 bits) 0.8 *** * ** * 0.6 ***** ** ** 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel GGGTGTGGCAGG consensus A G TCA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGKGGYMRG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 7.89158 E= 2.6e-002 -105 -1229 174 -263 -1229 -1229 199 -1229 -263 -207 184 -1229 17 -207 -265 132 -1229 -1229 199 -1229 -105 -365 60 95 -131 -1229 174 -205 -163 -265 181 -1229 -263 93 -33 17 53 43 -65 -83 27 -1229 110 -63 -263 -107 174 -1229 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGKGGYMRG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 50 E= 2.6e-002 0.120000 0.000000 0.840000 0.040000 0.000000 0.000000 1.000000 0.000000 0.040000 0.060000 0.900000 0.000000 0.280000 0.060000 0.040000 0.620000 0.000000 0.000000 1.000000 0.000000 0.120000 0.020000 0.380000 0.480000 0.100000 0.000000 0.840000 0.060000 0.080000 0.040000 0.880000 0.000000 0.040000 0.480000 0.200000 0.280000 0.360000 0.340000 0.160000 0.140000 0.300000 0.000000 0.540000 0.160000 0.040000 0.120000 0.840000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGKGGYMRG MEME-1 regular expression -------------------------------------------------------------------------------- GGG[TA]G[TG]GG[CTG][AC][GA]G -------------------------------------------------------------------------------- Time 0.43 secs. ******************************************************************************** ******************************************************************************** MOTIF RSAGASAGACAS MEME-2 width = 12 sites = 20 llr = 187 p-value = 5.1e-001 E-value = 5.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RSAGASAGACAS MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4273a:a:a37: pos.-specific C 14:1:6:3:714 probability G 65:614:8:1:6 matrix T ::31::::::3: bits 2.0 * * 1.8 * * * 1.6 * * * 1.4 * * * Relative 1.2 * * *** Entropy 1.0 * ***** * (13.5 bits) 0.8 * ******** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GGAGACAGACAG consensus ACTA G C ATC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSAGASAGACAS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 10.1871 E= 5.1e-001 49 -133 113 -1097 -73 67 84 -1097 149 -1097 -1097 27 1 -133 125 -231 193 -1097 -233 -1097 -1097 125 67 -1097 201 -1097 -1097 -1097 -1097 -1 158 -1097 201 -1097 -1097 -1097 27 137 -233 -1097 139 -233 -1097 27 -1097 67 125 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSAGASAGACAS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 20 E= 5.1e-001 0.350000 0.100000 0.550000 0.000000 0.150000 0.400000 0.450000 0.000000 0.700000 0.000000 0.000000 0.300000 0.250000 0.100000 0.600000 0.050000 0.950000 0.000000 0.050000 0.000000 0.000000 0.600000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.250000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.300000 0.650000 0.050000 0.000000 0.650000 0.050000 0.000000 0.300000 0.000000 0.400000 0.600000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RSAGASAGACAS MEME-2 regular expression -------------------------------------------------------------------------------- [GA][GC][AT][GA]A[CG]A[GC]A[CA][AT][GC] -------------------------------------------------------------------------------- Time 0.79 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************