******************************************************************************** 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/meme48 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun nz -w 12 -hsfrac 0.5 -shuf 2 -nostatus -mpi model: mod= zoops 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= 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 WGGGTGKGGCHB MEME-1 width = 12 sites = 60 llr = 591 p-value = 7.9e-005 E-value = 7.9e-005 ******************************************************************************** -------------------------------------------------------------------------------- Motif WGGGTGKGGCHB MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4:::1::11:22 pos.-specific C ::::1::::732 probability G 2aaa:a398:14 matrix T 5:::8:7:1342 bits 2.0 *** * 1.8 *** * 1.6 *** * 1.4 *** * * Relative 1.2 *** * * Entropy 1.0 ********* (14.2 bits) 0.8 ********* 0.6 ********** 0.4 ********** 0.2 *********** 0.0 ------------ Multilevel TGGGTGTGGCTG consensus A G TCC sequence AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGGTGKGGCHB MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 8.43276 E= 7.9e-005 63 -1255 -75 91 -1255 -1255 199 -1255 -1255 -1255 199 -1255 -1255 -1255 199 -1255 -131 -92 -1255 163 -1255 -1255 199 -1255 -1255 -1255 41 142 -131 -1255 178 -290 -190 -291 164 -109 -1255 144 -1255 35 -20 8 -159 80 -44 -22 67 -31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGGTGKGGCHB MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 60 E= 7.9e-005 0.383333 0.000000 0.150000 0.466667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.100000 0.133333 0.000000 0.766667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.333333 0.666667 0.100000 0.000000 0.866667 0.033333 0.066667 0.033333 0.783333 0.116667 0.000000 0.683333 0.000000 0.316667 0.216667 0.266667 0.083333 0.433333 0.183333 0.216667 0.400000 0.200000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WGGGTGKGGCHB MEME-1 regular expression -------------------------------------------------------------------------------- [TA]GGGTG[TG]GG[CT][TCA][GCT] -------------------------------------------------------------------------------- Time 0.81 secs. ******************************************************************************** ******************************************************************************** MOTIF YCYTATCTCTSM MEME-2 width = 12 sites = 79 llr = 552 p-value = 1.9e-001 E-value = 2.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCYTATCTCTSM MEME-2 Description -------------------------------------------------------------------------------- Simplified A 13::6::::1:3 pos.-specific C 56411:a17245 probability G ::::21::2:4: matrix T 316919:91722 bits 2.0 1.8 * 1.6 * 1.4 * Relative 1.2 * *** Entropy 1.0 * *** (10.1 bits) 0.8 ** ***** 0.6 *** ***** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCTTATCTCTGC consensus TAC G G CA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCYTATCTCTSM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 19507 bayes= 8.29344 E= 2.1e-001 -125 109 -261 36 11 131 -261 -190 -429 69 -331 116 -429 -131 -331 179 126 -151 -14 -149 -329 -273 -173 179 -1295 194 -331 -429 -329 -173 -273 179 -329 144 -6 -229 -129 -61 -431 154 -329 55 73 -39 35 90 -331 -39 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCYTATCTCTSM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 79 E= 2.1e-001 0.104411 0.534830 0.041159 0.319601 0.268968 0.623437 0.041159 0.066436 0.012658 0.405063 0.025316 0.556962 0.012658 0.101266 0.025316 0.860759 0.594937 0.088608 0.227848 0.088608 0.025316 0.037975 0.075949 0.860759 0.000000 0.962025 0.025316 0.012658 0.025316 0.075949 0.037975 0.860759 0.025316 0.683544 0.240506 0.050633 0.101266 0.164557 0.012658 0.721519 0.025316 0.367089 0.417722 0.189873 0.316456 0.468354 0.025316 0.189873 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCYTATCTCTSM MEME-2 regular expression -------------------------------------------------------------------------------- [CT][CA][TC]T[AG]TCT[CG]T[GC][CA] -------------------------------------------------------------------------------- Time 1.57 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************