******************************************************************************** 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= --none-- 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 -csites 30 common/Klf1-200-100.fa -oc results/meme9 -mod anr -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= anr nmotifs= 2 evt= inf objective function: em= E-value of product of p-values starts= E-value of product of p-values strands: + - width: minw= 8 maxw= 50 nsites: minsites= 2 maxsites= 30 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 trim: wg= 11 ws= 1 endgaps= yes data: n= 16900 N= 169 sample: seed= 0 hsfrac= 0 searchsize= 16900 norand= no csites= 30 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 RGCCACACCCW MEME-1 width = 11 sites = 30 llr = 350 E-value = 3.6e-026 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGCCACACCCW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 531:8:a:::5 pos.-specific C ::9a2a:aaa1 probability G 47::::::::: matrix T 1:1:::::::4 bits 2.0 * ***** 1.8 * ***** 1.6 * ***** 1.4 ******* Relative 1.2 ********* Entropy 1.0 ********* (16.8 bits) 0.8 ********* 0.6 ********** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel AGCCACACCCA consensus GA T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGCCACACCCW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 13237 bayes= 10.4897 E= 3.6e-026 101 -291 54 -131 10 -1155 154 -1155 -190 178 -1155 -190 -1155 199 -1155 -1155 175 -59 -1155 -1155 -1155 199 -1155 -1155 201 -1155 -1155 -1155 -1155 199 -1155 -1155 -1155 199 -1155 -1155 -1155 199 -1155 -1155 101 -92 -1155 56 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGCCACACCCW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 30 E= 3.6e-026 0.500000 0.033333 0.366667 0.100000 0.266667 0.000000 0.733333 0.000000 0.066667 0.866667 0.000000 0.066667 0.000000 1.000000 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.133333 0.000000 0.366667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGCCACACCCW MEME-1 regular expression -------------------------------------------------------------------------------- [AG][GA]CCACACCC[AT] -------------------------------------------------------------------------------- Time 3.29 secs. ******************************************************************************** ******************************************************************************** MOTIF SCTCCCHHTCTCTCCCCT MEME-2 width = 18 sites = 27 llr = 302 E-value = 2.8e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif SCTCCCHHTCTCTCCCCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:::2:34:3:1::1:12 pos.-specific C 49:868422738:86681 probability G 3::11:111::1:1:1:: matrix T 21a112337:7:a13217 bits 2.0 1.8 * * 1.6 * * 1.4 * * Relative 1.2 ** * *** Entropy 1.0 *** * * **** * (16.1 bits) 0.8 *** * ******* ** 0.6 *** * ********** 0.4 ***** ********** 0.2 ****************** 0.0 ------------------ Multilevel CCTCCCCATCTCTCCCCT consensus G A AT AC TT sequence TC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCTCCCHHTCTCTCCCCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 12054 bayes= 10.749 E= 2.8e-001 -174 82 24 -42 -274 176 -1140 -116 -1140 -1140 -276 195 -274 163 -176 -116 -16 124 -118 -174 -1140 170 -1140 -42 25 56 -176 6 58 -18 -118 25 -1140 -44 -176 158 6 141 -276 -274 -1140 4 -1140 158 -174 170 -118 -1140 -1140 -276 -1140 195 -1140 163 -176 -75 -174 132 -1140 25 -274 132 -118 -16 -116 163 -1140 -116 -42 -76 -1140 142 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCTCCCHHTCTCTCCCCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 27 E= 2.8e-001 0.074074 0.444444 0.296296 0.185185 0.037037 0.851852 0.000000 0.111111 0.000000 0.000000 0.037037 0.962963 0.037037 0.777778 0.074074 0.111111 0.222222 0.592593 0.111111 0.074074 0.000000 0.814815 0.000000 0.185185 0.296296 0.370370 0.074074 0.259259 0.370370 0.222222 0.111111 0.296296 0.000000 0.185185 0.074074 0.740741 0.259259 0.666667 0.037037 0.037037 0.000000 0.259259 0.000000 0.740741 0.074074 0.814815 0.111111 0.000000 0.000000 0.037037 0.000000 0.962963 0.000000 0.777778 0.074074 0.148148 0.074074 0.629630 0.000000 0.296296 0.037037 0.629630 0.111111 0.222222 0.111111 0.777778 0.000000 0.111111 0.185185 0.148148 0.000000 0.666667 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SCTCCCHHTCTCTCCCCT MEME-2 regular expression -------------------------------------------------------------------------------- [CG]CTC[CA]C[CAT][ATC]T[CA][TC]CTC[CT][CT]CT -------------------------------------------------------------------------------- Time 6.54 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************