******************************************************************************** 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/meme8 -mod zoops -dna -revcomp -brief 0 -nmotifs 2 -objfun classic -minw 8 -nostatus -mpi model: mod= zoops 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= 169 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 WCVCCSTGSACYTTGTTT MEME-1 width = 18 sites = 8 llr = 102 E-value = 2.4e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif WCVCCSTGSACYTTGTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4:4::1:1:61::::11: pos.-specific C :83994:341653::331 probability G :331:4:6513:1:a::: matrix T 6:1:11a:11:56a:669 bits 2.0 * ** 1.8 * ** 1.6 * ** 1.4 ** * ** * Relative 1.2 * ** * ** * Entropy 1.0 ** ** * * ** * (18.4 bits) 0.8 ** ** * ******* 0.6 ** ** *** ******** 0.4 ** ** ************ 0.2 ** *************** 0.0 ------------------ Multilevel TCACCCTGGACCTTGTTT consensus AGC G CC GTC CC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCVCCSTGSACYTTGTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 12054 bayes= 9.7075 E= 2.4e+000 59 -965 -965 133 -965 157 -1 -965 59 -1 -1 -99 -965 180 -101 -965 -965 180 -965 -99 -99 58 58 -99 -965 -965 -965 201 -99 -1 131 -965 -965 58 99 -99 133 -101 -101 -99 -99 131 -1 -965 -965 99 -965 101 -965 -1 -101 133 -965 -965 -965 201 -965 -965 199 -965 -99 -1 -965 133 -99 -1 -965 133 -965 -101 -965 182 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCVCCSTGSACYTTGTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 8 E= 2.4e+000 0.375000 0.000000 0.000000 0.625000 0.000000 0.750000 0.250000 0.000000 0.375000 0.250000 0.250000 0.125000 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.125000 0.125000 0.375000 0.375000 0.125000 0.000000 0.000000 0.000000 1.000000 0.125000 0.250000 0.625000 0.000000 0.000000 0.375000 0.500000 0.125000 0.625000 0.125000 0.125000 0.125000 0.125000 0.625000 0.250000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.250000 0.125000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.125000 0.250000 0.000000 0.625000 0.125000 0.250000 0.000000 0.625000 0.000000 0.125000 0.000000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCVCCSTGSACYTTGTTT MEME-1 regular expression -------------------------------------------------------------------------------- [TA][CG][ACG]CC[CG]T[GC][GC]A[CG][CT][TC]TG[TC][TC]T -------------------------------------------------------------------------------- Time 0.68 secs. ******************************************************************************** ******************************************************************************** MOTIF CCAACCACCTYYCCC MEME-2 width = 15 sites = 4 llr = 66 E-value = 1.9e+004 ******************************************************************************** -------------------------------------------------------------------------------- Motif CCAACCACCTYYCCC MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::883:a:::::::: pos.-specific C 88338a:aa:55aaa probability G 3:::::::::::::: matrix T :3:::::::a55::: bits 2.0 ***** *** 1.8 ***** *** 1.6 ***** *** 1.4 ***** *** Relative 1.2 ********** *** Entropy 1.0 *************** (23.9 bits) 0.8 *************** 0.6 *************** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel CCAACCACCTCCCCC consensus GTCCA TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAACCACCTYYCCC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 12561 bayes= 11.6162 E= 1.9e+004 -865 157 -1 -865 -865 157 -865 1 159 -1 -865 -865 159 -1 -865 -865 1 157 -865 -865 -865 199 -865 -865 201 -865 -865 -865 -865 199 -865 -865 -865 199 -865 -865 -865 -865 -865 201 -865 99 -865 101 -865 99 -865 101 -865 199 -865 -865 -865 199 -865 -865 -865 199 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAACCACCTYYCCC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4 E= 1.9e+004 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.250000 0.750000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.250000 0.750000 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 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CCAACCACCTYYCCC MEME-2 regular expression -------------------------------------------------------------------------------- [CG][CT][AC][AC][CA]CACCT[CT][CT]CCC -------------------------------------------------------------------------------- Time 1.29 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: Timothys-Mac-Mini.local ********************************************************************************