******************************************************************************** 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.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 common/Klf1-200.fa -oc results/meme38 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun cd -maxw 30 -searchsize 40000 -norand -nostatus -mpi model: mod= zoops nmotifs= 2 evt= inf objective function: em= Central Enrichment: p-value of mean distance starts= Mean distance of best site from center strands: + - width: minw= 8 maxw= 30 nsites: minsites= 2 maxsites= 200 wnsites= 0.8 theta: spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 100000 N= 200 sample: seed= 0 hsfrac= 0.5 searchsize= 40000 norand= yes csites= -1 Letter frequencies in dataset: A 0.256 C 0.244 G 0.244 T 0.256 Background letter frequencies (from file dataset with add-one prior applied): A 0.256 C 0.244 G 0.244 T 0.256 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF GCCACACCCWKCYNNBH MEME-1 width = 17 sites = 148 llr = 1308 p-value = 5.1e-004 E-value = 5.1e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GCCACACCCWKCYNNBH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 32:8:7:1:51222213 pos.-specific C 1692a:a9a11533443 probability G 61:::2::::4112221 matrix T ::1::1:::43253234 bits 2.0 * 1.8 * * 1.6 * * * 1.4 * * *** Relative 1.2 * * *** Entropy 1.0 *** *** (12.8 bits) 0.8 ******* 0.6 ********* 0.4 ********** 0.2 ************* ** 0.0 ----------------- Multilevel GCCACACCCAGCTTCCT consensus A G TT CCATC sequence GTGA AG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACACCCWKCYNNBH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 68385 bayes= 9.4654 E= 5.1e-004 5 -117 125 -241 -41 136 -88 -241 -241 185 -1302 -183 161 -34 -433 -441 -441 198 -433 -441 142 -433 -17 -160 -441 202 -1302 -1302 -183 187 -433 -341 -341 197 -1302 -341 99 -170 -636 69 -105 -72 67 41 -68 110 -98 -39 -68 14 -148 92 -28 15 -5 14 -20 54 -21 -28 -128 78 -19 3 -3 10 -159 67 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACACCCWKCYNNBH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 148 E= 5.1e-004 0.265060 0.108434 0.578313 0.048193 0.192771 0.626506 0.132530 0.048193 0.048193 0.879518 0.000000 0.072289 0.783133 0.192771 0.012048 0.012048 0.012048 0.963855 0.012048 0.012048 0.686747 0.012048 0.216867 0.084337 0.012048 0.987952 0.000000 0.000000 0.072289 0.891566 0.012048 0.024096 0.024096 0.951807 0.000000 0.024096 0.509112 0.075225 0.002936 0.412726 0.123570 0.147515 0.388478 0.340437 0.159714 0.521009 0.123418 0.195859 0.159714 0.267997 0.087274 0.485016 0.210995 0.270933 0.234788 0.283284 0.223043 0.355270 0.210692 0.210995 0.105649 0.418447 0.213628 0.262276 0.250227 0.261821 0.081098 0.406854 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GCCACACCCWKCYNNBH MEME-1 regular expression -------------------------------------------------------------------------------- [GA]CCAC[AG]CCC[AT][GT]C[TC][TCGA][CATG][CTG][TCA] -------------------------------------------------------------------------------- Time 3.37 secs. ******************************************************************************** ******************************************************************************** MOTIF SAAWCCMCAYY MEME-2 width = 11 sites = 40 llr = 350 p-value = 2.9e-001 E-value = 3.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif SAAWCCMCAYY MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a94::5:a11 pos.-specific C 6:129a5a:34 probability G 4::::::::11 matrix T :::5:::::64 bits 2.0 1.8 * * 1.6 * ** ** 1.4 * ** ** Relative 1.2 ** ** ** Entropy 1.0 ** ** ** (12.6 bits) 0.8 *** ***** 0.6 *** ***** 0.4 ********** 0.2 *********** 0.0 ----------- Multilevel CAATCCACATC consensus G A C CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SAAWCCMCAYY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 69585 bayes= 11.9323 E= 3.4e-001 -463 122 75 -463 192 -463 -463 -463 173 -144 -229 -463 53 -52 -463 81 -268 192 -1129 -268 -268 198 -1129 -1129 90 98 -1129 -268 -1129 198 -260 -1129 190 -260 -1129 -1129 -235 25 -144 115 -150 75 -91 53 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SAAWCCMCAYY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 40 E= 3.4e-001 0.010252 0.569748 0.409748 0.010252 0.970252 0.009748 0.009748 0.010252 0.850252 0.089748 0.049748 0.010252 0.370252 0.169748 0.009748 0.450252 0.040000 0.920000 0.000000 0.040000 0.040000 0.960000 0.000000 0.000000 0.480000 0.480000 0.000000 0.040000 0.000000 0.960000 0.040000 0.000000 0.960000 0.040000 0.000000 0.000000 0.050252 0.289748 0.089748 0.570252 0.090252 0.409748 0.129748 0.370252 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif SAAWCCMCAYY MEME-2 regular expression -------------------------------------------------------------------------------- [CG]AA[TA]CC[AC]CA[TC][CT] -------------------------------------------------------------------------------- Time 6.51 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************