******************************************************************************** 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/meme47 -mod oops -dna -revcomp -brief 0 -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= oops nmotifs= 2 evt= inf objective function: em= Noise-injected 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= 0.5 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 NMWGGGTGKGGY MEME-1 width = 12 sites = 169 llr = 895 p-value = 3.3e-003 E-value = 3.3e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif NMWGGGTGKGGY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 225:1:211211 pos.-specific C 24:::12:::25 probability G 32:988183661 matrix T 215:1:516213 bits 2.0 1.8 1.6 1.4 * Relative 1.2 * * Entropy 1.0 *** * (7.6 bits) 0.8 *** * 0.6 **** *** 0.4 ********** 0.2 *********** 0.0 ------------ Multilevel GCTGGGTGTGGC consensus TAA C G T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NMWGGGTGKGGY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 6.24988 E= 3.3e-003 -11 -46 47 -7 0 76 -41 -87 89 -440 -241 95 -281 -440 187 -281 -178 -370 171 -156 -254 -148 173 -300 -61 -18 -176 112 -178 -255 166 -146 -113 -423 33 117 -72 -295 137 -56 -81 -65 121 -107 -139 98 -141 34 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NMWGGGTGKGGY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 3.3e-003 0.230696 0.183506 0.349186 0.236613 0.248447 0.426109 0.189423 0.136021 0.461465 0.011908 0.047411 0.479216 0.035429 0.011908 0.917233 0.035429 0.072402 0.019314 0.824047 0.084237 0.042816 0.090320 0.835882 0.030982 0.162667 0.221949 0.074020 0.541365 0.072439 0.042945 0.794425 0.090191 0.113859 0.013360 0.315135 0.557646 0.150832 0.032600 0.647984 0.168584 0.141938 0.159837 0.579955 0.118269 0.094601 0.497115 0.094748 0.313536 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NMWGGGTGKGGY MEME-1 regular expression -------------------------------------------------------------------------------- [GTA][CA][TA]GGG[TC]G[TG]GG[CT] -------------------------------------------------------------------------------- Time 0.71 secs. ******************************************************************************** ******************************************************************************** MOTIF RCWGAGCAGAGA MEME-2 width = 12 sites = 169 llr = 716 p-value = 3.6e-001 E-value = 3.6e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCWGAGCAGAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 525252281727 pos.-specific C 1511116:1:21 probability G 3216352:7151 matrix T 113111:1:121 bits 2.0 1.8 1.6 1.4 Relative 1.2 * Entropy 1.0 * (6.1 bits) 0.8 *** 0.6 *** * 0.4 * *** **** * 0.2 ************ 0.0 ------------ Multilevel ACAGAGCAGAGA consensus G TAG A C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCWGAGCAGAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 6.24988 E= 3.6e-001 108 -171 21 -122 -43 104 -40 -120 107 -195 -150 39 -31 -95 118 -131 110 -195 5 -81 -39 -89 111 -93 -17 122 -69 -275 177 -381 -381 -107 -93 -124 153 -281 157 -282 -76 -169 -44 -32 88 -69 148 -143 -90 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCWGAGCAGAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 169 E= 3.6e-001 0.526517 0.077034 0.290051 0.106398 0.184791 0.516392 0.190948 0.107868 0.520599 0.065199 0.088868 0.325333 0.201073 0.130288 0.568158 0.100481 0.532434 0.065199 0.260466 0.141901 0.189239 0.136205 0.544489 0.130067 0.220294 0.587398 0.155445 0.036862 0.846043 0.017862 0.017862 0.118233 0.130067 0.106619 0.727921 0.035392 0.739534 0.035614 0.148040 0.076813 0.183321 0.201294 0.461649 0.153736 0.690727 0.093297 0.134717 0.081260 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCWGAGCAGAGA MEME-2 regular expression -------------------------------------------------------------------------------- [AG]C[AT][GA][AG]G[CA]AGA[GC]A -------------------------------------------------------------------------------- Time 1.31 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************