******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 5.4.1 (Release date: Sat Aug 21 19:23:23 2021 -0700) 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= seqs/AT5G65310_peak_sequences.fasta 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 seqs/AT5G65310_peak_sequences.fasta -dna -oc out/AT5G65310 -nostatus -time 300 -mod zoops -nmotifs 2 -minw 6 -maxw 50 -objfun classic -revcomp -markov_order 0 -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= 6 maxw= 50 nsites: minsites= 2 maxsites= 7904 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= 2264314 N= 7904 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.371 C 0.129 G 0.129 T 0.371 Background letter frequencies (from file dataset with add-one prior applied): A 0.372 C 0.128 G 0.128 T 0.372 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AATWATTGDTTTDDD MEME-1 width = 15 sites = 7826 llr = 52556 E-value = 4.9e-052 ******************************************************************************** -------------------------------------------------------------------------------- Motif AATWATTGDTTTDDD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 9a:3a::23222333 pos.-specific C 1::1::::1111111 probability G :::2:::63121222 matrix T ::a5:aa23555434 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 ** *** (9.7 bits) 1.2 ** *** 0.9 *** **** 0.6 *** **** 0.3 *** **** 0.0 --------------- Multilevel AATTATTGATTTTTT consensus A TTAG AAA sequence G GGG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATWATTGDTTTDDD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2153657 bayes= 10.2476 E= 4.9e-052 128 -116 -1958 -325 143 -1958 -1958 -1958 -1958 -1958 -1958 143 -56 -3 38 29 143 -1958 -1958 -1958 -1958 -1958 -1958 143 -1958 -1958 -1958 143 -108 -1958 218 -62 -12 -109 106 -18 -70 3 19 41 -94 -18 71 38 -92 10 11 51 -32 -15 73 1 -27 5 75 -12 -46 -24 86 6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATWATTGDTTTDDD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7826 E= 4.9e-052 0.903399 0.057501 0.000000 0.039100 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.252364 0.125479 0.166369 0.455788 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.176208 0.000000 0.582418 0.241375 0.343087 0.060184 0.268081 0.328648 0.228086 0.130718 0.146563 0.494633 0.193713 0.112957 0.209430 0.483900 0.196397 0.137363 0.138129 0.528111 0.297726 0.115257 0.212369 0.374649 0.309098 0.133146 0.214925 0.342832 0.270381 0.108868 0.231919 0.388832 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AATWATTGDTTTDDD MEME-1 regular expression -------------------------------------------------------------------------------- AAT[TA]ATT[GT][ATG][TA][TG]T[TAG][TAG][TAG] -------------------------------------------------------------------------------- Time 75.91 secs. ******************************************************************************** ******************************************************************************** MOTIF GATTATAATCATCAAACCGYAGAGATATTTGATAGCA MEME-2 width = 37 sites = 2 llr = 96 E-value = 2.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GATTATAATCATCAAACCGYAGAGATATTTGATAGCA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a::a:aa::a::aaa::::a:a:a:a::::a:a::a pos.-specific C :::::::::a::a:::aa:5:::::::::::::::a: probability G a:::::::::::::::::a::a:a::::::a:::a:: matrix T ::aa:a::a::a:::::::5:::::a:aaa::a:::: bits 3.0 * * * *** * * * ** 2.7 * * * *** * * * ** 2.4 * * * *** * * * ** 2.1 * * * *** * * * ** Relative 1.8 * * * *** * * * ** Entropy 1.5 ******************* ***************** (69.5 bits) 1.2 ************************************* 0.9 ************************************* 0.6 ************************************* 0.3 ************************************* 0.0 ------------------------------------- Multilevel GATTATAATCATCAAACCGCAGAGATATTTGATAGCA consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATTATAATCATCAAACCGYAGAGATATTTGATAGCA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 37 n= 1979769 bayes= 18.1514 E= 2.7e-004 -765 -765 296 -765 142 -765 -765 -765 -765 -765 -765 142 -765 -765 -765 142 142 -765 -765 -765 -765 -765 -765 142 142 -765 -765 -765 142 -765 -765 -765 -765 -765 -765 142 -765 296 -765 -765 142 -765 -765 -765 -765 -765 -765 142 -765 296 -765 -765 142 -765 -765 -765 142 -765 -765 -765 142 -765 -765 -765 -765 296 -765 -765 -765 296 -765 -765 -765 -765 296 -765 -765 196 -765 43 142 -765 -765 -765 -765 -765 296 -765 142 -765 -765 -765 -765 -765 296 -765 142 -765 -765 -765 -765 -765 -765 142 142 -765 -765 -765 -765 -765 -765 142 -765 -765 -765 142 -765 -765 -765 142 -765 -765 296 -765 142 -765 -765 -765 -765 -765 -765 142 142 -765 -765 -765 -765 -765 296 -765 -765 296 -765 -765 142 -765 -765 -765 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATTATAATCATCAAACCGYAGAGATATTTGATAGCA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 37 nsites= 2 E= 2.7e-004 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 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 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.000000 0.500000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 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 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GATTATAATCATCAAACCGYAGAGATATTTGATAGCA MEME-2 regular expression -------------------------------------------------------------------------------- GATTATAATCATCAAACCG[CT]AGAGATATTTGATAGCA -------------------------------------------------------------------------------- Time 145.82 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************