******************************************************************************** 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/meme36 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= Selective 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 GGTGTGGYCKGV MEME-1 width = 12 sites = 31 llr = 289 p-value = 3.5e-003 E-value = 3.5e-003 ******************************************************************************** -------------------------------------------------------------------------------- Motif GGTGTGGYCKGV MEME-1 Description -------------------------------------------------------------------------------- Simplified A ::::2:::21:2 pos.-specific C :3::::255::4 probability G a7:a298124a4 matrix T ::a:61:415:: 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 GGTGTGGCCTGC consensus C A TAG G sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGTGGYCKGV MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 9.25185 E= 3.5e-003 -1160 -1160 194 -294 -1160 21 150 -1160 -294 -1160 -1160 196 -1160 -296 194 -1160 -14 -1160 -38 122 -1160 -296 184 -194 -294 -64 168 -1160 -1160 112 -196 64 -14 112 -64 -194 -94 -1160 62 96 -1160 -1160 194 -294 -30 65 53 -262 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGTGGYCKGV MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 31 E= 3.5e-003 0.000000 0.000000 0.967742 0.032258 0.000000 0.290323 0.709677 0.000000 0.032258 0.000000 0.000000 0.967742 0.000000 0.032258 0.967742 0.000000 0.225806 0.000000 0.193548 0.580645 0.000000 0.032258 0.903226 0.064516 0.032258 0.161290 0.806452 0.000000 0.000000 0.548387 0.064516 0.387097 0.225806 0.548387 0.161290 0.064516 0.129032 0.000000 0.387097 0.483871 0.000000 0.000000 0.967742 0.032258 0.201563 0.395212 0.362953 0.040272 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GGTGTGGYCKGV MEME-1 regular expression -------------------------------------------------------------------------------- G[GC]TG[TA]GG[CT][CA][TG]G[CGA] -------------------------------------------------------------------------------- Time 0.42 secs. ******************************************************************************** ******************************************************************************** MOTIF CCYTGYCYCTTC MEME-2 width = 12 sites = 18 llr = 173 p-value = 6.9e-001 E-value = 6.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCYTGYCYCTTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :1:1:::::::2 pos.-specific C 974:3376a:16 probability G 1:::72::::31 matrix T :2691534:a72 bits 2.0 ** 1.8 ** 1.6 * ** 1.4 * * ** Relative 1.2 * * * ** Entropy 1.0 * ** **** (13.9 bits) 0.8 ***** ***** 0.6 *********** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CCTTGTCCCTTC consensus C CCTT G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCYTGYCYCTTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 13068 bayes= 8.19635 E= 6.9e-001 -1081 191 -218 -1081 -116 152 -1081 -58 -1081 63 -1081 130 -116 -1081 -1081 184 -1081 14 141 -216 -1081 41 -59 101 -1081 152 -1081 16 -1081 128 -1081 65 -1081 199 -1081 -1081 -1081 -1081 -1081 201 -1081 -218 14 142 -58 114 -118 -58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCYTGYCYCTTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 6.9e-001 0.000000 0.944444 0.055556 0.000000 0.111111 0.722222 0.000000 0.166667 0.000000 0.388889 0.000000 0.611111 0.111111 0.000000 0.000000 0.888889 0.000000 0.277778 0.666667 0.055556 0.000000 0.333333 0.166667 0.500000 0.000000 0.722222 0.000000 0.277778 0.000000 0.611111 0.000000 0.388889 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.055556 0.277778 0.666667 0.166667 0.555556 0.111111 0.166667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCYTGYCYCTTC MEME-2 regular expression -------------------------------------------------------------------------------- CC[TC]T[GC][TC][CT][CT]CT[TG]C -------------------------------------------------------------------------------- Time 0.79 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************