******************************************************************************** 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/meme35 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= Selective 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 CWGGGTGTGGYY MEME-1 width = 12 sites = 42 llr = 454 p-value = 3.0e-008 E-value = 3.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif CWGGGTGTGGYY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 14:::::::1:2 pos.-specific C 6::::1:::163 probability G 1:aaa:a1a7:1 matrix T 16:::8:9:134 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 CTGGGTGTGGCT consensus A TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGGGTGTGGYY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.30462 E= 3.0e-008 -80 118 -82 -80 70 -1204 -340 120 -1204 -1204 199 -1204 -1204 -1204 196 -338 -1204 -1204 199 -1204 -238 -108 -1204 175 -1204 -1204 199 -1204 -1204 -1204 -108 183 -1204 -1204 199 -1204 -180 -182 155 -106 -338 135 -1204 42 -58 41 -140 70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGGGTGTGGYY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 42 E= 3.0e-008 0.142857 0.571429 0.142857 0.142857 0.404762 0.000000 0.023810 0.571429 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.976190 0.023810 0.000000 0.000000 1.000000 0.000000 0.047619 0.119048 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.119048 0.880952 0.000000 0.000000 1.000000 0.000000 0.071429 0.071429 0.738095 0.119048 0.023810 0.642857 0.000000 0.333333 0.166667 0.333333 0.095238 0.404762 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CWGGGTGTGGYY MEME-1 regular expression -------------------------------------------------------------------------------- C[TA]GGGTGTGG[CT][TC] -------------------------------------------------------------------------------- Time 0.33 secs. ******************************************************************************** ******************************************************************************** MOTIF CTCCYTCTSCCY MEME-2 width = 12 sites = 33 llr = 273 p-value = 4.1e-001 E-value = 4.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCCYTCTSCCY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 12:2:2::::1: pos.-specific C 8:88628:4873 probability G 1:2:::1:51:: matrix T 17::461a1127 bits 2.0 * 1.8 * 1.6 * 1.4 * Relative 1.2 * Entropy 1.0 *** ** * * (11.9 bits) 0.8 ***** ** *** 0.6 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTCCCTCTGCCT consensus AGAT C TC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCYTCTSCCY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.39895 E= 4.1e-001 -203 159 -205 -103 -4 -1169 -305 155 -1169 159 -25 -303 -23 159 -1169 -303 -303 127 -1169 55 -45 -47 -305 129 -303 165 -205 -103 -1169 -1169 -1169 201 -1169 75 85 -103 -1169 165 -147 -103 -203 147 -1169 -4 -1169 41 -1169 142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCYTCTSCCY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 33 E= 4.1e-001 0.060606 0.757576 0.060606 0.121212 0.242424 0.000000 0.030303 0.727273 0.000000 0.757576 0.212121 0.030303 0.212121 0.757576 0.000000 0.030303 0.030303 0.606061 0.000000 0.363636 0.181818 0.181818 0.030303 0.606061 0.030303 0.787879 0.060606 0.121212 0.000000 0.000000 0.000000 1.000000 0.000000 0.424242 0.454545 0.121212 0.000000 0.787879 0.090909 0.121212 0.060606 0.696970 0.000000 0.242424 0.000000 0.333333 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCYTCTSCCY MEME-2 regular expression -------------------------------------------------------------------------------- C[TA][CG][CA][CT]TCT[GC]C[CT][TC] -------------------------------------------------------------------------------- Time 0.62 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************