******************************************************************************** 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/meme26 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun de -w 12 -hsfrac 0.6 -shuf 3 -nostatus -mpi model: mod= zoops 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= 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 GGGTGKGGYNGG MEME-1 width = 12 sites = 71 llr = 600 p-value = 9.2e-004 E-value = 9.2e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGGTGKGGYNGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::2:111:321 pos.-specific C :::1:::16311 probability G a9a:a4991256 matrix T :1:7:5::3222 bits 2.0 * 1.8 * * 1.6 *** * 1.4 *** * Relative 1.2 *** * ** Entropy 1.0 *** * ** (12.2 bits) 0.8 ***** ** 0.6 ********* 0.4 ********* * 0.2 ********* ** 0.0 ------------ Multilevel GGGTGTGGCAGG consensus G TCA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGKGGYNGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.11396 E= 9.2e-004 -414 -1279 193 -314 -1279 -1279 189 -182 -314 -1279 195 -1279 -33 -184 -316 150 -1279 -1279 199 -1279 -156 -416 54 111 -182 -316 180 -314 -214 -184 177 -414 -314 120 -184 38 25 23 -16 -44 -23 -135 105 -56 -82 -99 116 -56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGKGGYNGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 71 E= 9.2e-004 0.014085 0.000000 0.957746 0.028169 0.000000 0.000000 0.929577 0.070423 0.028169 0.000000 0.971831 0.000000 0.197183 0.070423 0.028169 0.704225 0.000000 0.000000 1.000000 0.000000 0.084507 0.014085 0.366197 0.535211 0.070423 0.028169 0.873239 0.028169 0.056338 0.070423 0.859155 0.014085 0.028169 0.577465 0.070423 0.323944 0.295775 0.295775 0.225352 0.183099 0.211268 0.098592 0.521127 0.169014 0.140845 0.126761 0.563380 0.169014 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGGTGKGGYNGG MEME-1 regular expression -------------------------------------------------------------------------------- GGGTG[TG]GG[CT][ACG][GA]G -------------------------------------------------------------------------------- Time 0.34 secs. ******************************************************************************** ******************************************************************************** MOTIF AGRAGRCARRSC MEME-2 width = 12 sites = 18 llr = 183 p-value = 7.4e-002 E-value = 7.4e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGRAGRCARRSC MEME-2 Description -------------------------------------------------------------------------------- Simplified A a35924:a35:1 pos.-specific C ::1::2a:2:48 probability G :74184::556: matrix T :::1:::::::2 bits 2.0 * ** 1.8 * ** 1.6 * ** 1.4 * * ** Relative 1.2 ** ** ** Entropy 1.0 ** ** ** *** (14.6 bits) 0.8 ***** ** *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel AGAAGGCAGAGC consensus AG AA AGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAGRCARRSC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.42162 E= 7.4e-002 201 -1081 -1081 -1081 16 -1081 152 -1081 101 -218 82 -1081 184 -1081 -218 -216 -16 -1081 163 -1081 65 -59 82 -1081 -1081 199 -1081 -1081 201 -1081 -1081 -1081 42 -59 99 -1081 101 -1081 99 -1081 -1081 82 114 -1081 -216 163 -1081 -58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAGRCARRSC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 7.4e-002 1.000000 0.000000 0.000000 0.000000 0.277778 0.000000 0.722222 0.000000 0.500000 0.055556 0.444444 0.000000 0.888889 0.000000 0.055556 0.055556 0.222222 0.000000 0.777778 0.000000 0.388889 0.166667 0.444444 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.166667 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.444444 0.555556 0.000000 0.055556 0.777778 0.000000 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGRAGRCARRSC MEME-2 regular expression -------------------------------------------------------------------------------- A[GA][AG]A[GA][GA]CA[GA][AG][GC]C -------------------------------------------------------------------------------- Time 0.62 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************