******************************************************************************** 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/AT5G03790_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/AT5G03790_peak_sequences.fasta -dna -oc out/AT5G03790 -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= 8666 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= 2511722 N= 8666 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.372 C 0.128 G 0.128 T 0.372 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 HMAATAATTDW MEME-1 width = 11 sites = 8639 llr = 60968 E-value = 1.8e-068 ******************************************************************************** -------------------------------------------------------------------------------- Motif HMAATAATTDW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33aa:aa:135 pos.-specific C 35:::::::21 probability G 1:::::::231 matrix T 32::a::a723 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 *** ** (10.2 bits) 1.2 ****** 0.9 ****** 0.6 ******** 0.3 ********* 0.0 ----------- Multilevel ACAATAATTGA consensus TA AT sequence CT T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HMAATAATTDW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2425062 bayes= 10.2921 E= 1.8e-068 -9 102 -10 -46 -54 196 -1972 -59 143 -1972 -1972 -1972 143 -1972 -1972 -1972 -1972 -1972 -1972 143 140 -1972 -1972 -449 143 -1972 -1972 -1972 -1972 -1972 -1972 143 -201 -1972 35 100 -55 38 143 -67 51 -21 -41 -49 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HMAATAATTDW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 8639 E= 1.8e-068 0.349346 0.260678 0.119806 0.270170 0.255469 0.497627 0.000000 0.246904 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.983447 0.000000 0.000000 0.016553 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.092256 0.000000 0.163445 0.744299 0.253849 0.167265 0.344600 0.234286 0.527955 0.110429 0.096307 0.265308 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HMAATAATTDW MEME-1 regular expression -------------------------------------------------------------------------------- [ATC][CAT]AATAATT[GAT][AT] -------------------------------------------------------------------------------- Time 71.28 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTAACCCGCGGTAYACC MEME-2 width = 18 sites = 34 llr = 795 E-value = 3.6e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTAACCCGCGGTAYACC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 12:9a::::::::a:9:: pos.-specific C :::1:9aa:a:1::51a9 probability G 1::1::::a:a9:::1:: matrix T 88a::1:::::1a:5::: bits 3.0 **** * 2.7 ***** ** 2.4 ***** ** 2.1 ******* ** Relative 1.8 ******* ** Entropy 1.5 ******* ** (33.7 bits) 1.2 * ********** ** 0.9 ***************** 0.6 ****************** 0.3 ****************** 0.0 ------------------ Multilevel TTTAACCCGCGGTACACC consensus T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTAACCCGCGGTAYACC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 18 n= 2364400 bayes= 17.4506 E= 3.6e-004 -166 -1173 -112 115 -108 -1173 -1173 115 -1173 -1173 -212 138 120 -112 -54 -1173 138 -212 -1173 -1173 -1173 273 -1173 -134 -1173 296 -1173 -1173 -1173 296 -1173 -1173 -1173 -1173 296 -1173 -1173 296 -1173 -1173 -1173 -212 292 -1173 -366 -112 273 -266 -1173 -212 -1173 138 138 -1173 -212 -1173 -366 196 -1173 34 125 -112 -112 -1173 -1173 296 -1173 -1173 -1173 288 -212 -366 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTAACCCGCGGTAYACC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 18 nsites= 34 E= 3.6e-004 0.117647 0.000000 0.058824 0.823529 0.176471 0.000000 0.000000 0.823529 0.000000 0.000000 0.029412 0.970588 0.852941 0.058824 0.088235 0.000000 0.970588 0.029412 0.000000 0.000000 0.000000 0.852941 0.000000 0.147059 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 1.000000 0.000000 0.000000 0.000000 0.029412 0.970588 0.000000 0.029412 0.058824 0.852941 0.058824 0.000000 0.029412 0.000000 0.970588 0.970588 0.000000 0.029412 0.000000 0.029412 0.500000 0.000000 0.470588 0.882353 0.058824 0.058824 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.941176 0.029412 0.029412 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTAACCCGCGGTAYACC MEME-2 regular expression -------------------------------------------------------------------------------- TTTAACCCGCGGTA[CT]ACC -------------------------------------------------------------------------------- Time 138.47 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************