******************************************************************************** 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/AT2G20400_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/AT2G20400_peak_sequences.fasta -dna -oc out/AT2G20400 -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= 2191 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= 396884 N= 2191 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.334 C 0.166 G 0.166 T 0.334 Background letter frequencies (from file dataset with add-one prior applied): A 0.336 C 0.164 G 0.164 T 0.336 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DAGAATATTCB MEME-1 width = 11 sites = 2110 llr = 16657 E-value = 3.1e-455 ******************************************************************************** -------------------------------------------------------------------------------- Motif DAGAATATTCB MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4526a:a:1:: pos.-specific C 21:1:::::a4 probability G 2281:2::1:3 matrix T 2212:8:a8:3 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.6 ** * Entropy 1.3 * * ** * (11.4 bits) 1.0 * **** * 0.8 * ******* 0.5 * ******* 0.3 ********** 0.0 ----------- Multilevel AAGAATATTCC consensus T G sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAGAATATTCB MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 374974 bayes= 8.81348 E= 3.1e-455 14 0 49 -52 65 -29 18 -113 -102 -374 222 -255 85 -78 -16 -115 153 -685 -1769 -349 -1769 -685 11 129 156 -1769 -585 -530 -1769 -1769 -585 157 -203 -312 -152 133 -1769 261 -1769 -1769 -577 144 75 -30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAGAATATTCB MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2110 E= 3.1e-455 0.371090 0.163981 0.231280 0.233649 0.526066 0.134597 0.185782 0.153555 0.165403 0.012322 0.764929 0.057346 0.605687 0.095735 0.146919 0.151659 0.968720 0.001422 0.000000 0.029858 0.000000 0.001422 0.177725 0.820853 0.988626 0.000000 0.002844 0.008531 0.000000 0.000000 0.002844 0.997156 0.082464 0.018957 0.057346 0.841232 0.000000 1.000000 0.000000 0.000000 0.006161 0.445498 0.276303 0.272038 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAGAATATTCB MEME-1 regular expression -------------------------------------------------------------------------------- [ATG]AGAATATTC[CGT] -------------------------------------------------------------------------------- Time 120.66 secs. ******************************************************************************** ******************************************************************************** MOTIF CAAAACTTATATAACACAGAGATTTGATA MEME-2 width = 29 sites = 19 llr = 683 E-value = 1.5e-030 ******************************************************************************** -------------------------------------------------------------------------------- Motif CAAAACTTATATAACACAGAGATTTGATA MEME-2 Description -------------------------------------------------------------------------------- Simplified A :aaaa:::a:a:aa:a:a:a1a::1:a:a pos.-specific C a::::a::::::::a:a:::::::::::: probability G ::::::::::::::::::a:9::::9::: matrix T ::::::aa:a:a::::::::::aa91:a: bits 2.6 * * * * * 2.3 * * * * * * * 2.1 * * * * * * * 1.8 * * * * * * * Relative 1.6 ************************ **** Entropy 1.3 ***************************** (51.9 bits) 1.0 ***************************** 0.8 ***************************** 0.5 ***************************** 0.3 ***************************** 0.0 ----------------------------- Multilevel CAAAACTTATATAACACAGAGATTTGATA consensus sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAAACTTATATAACACAGAGATTTGATA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 335536 bayes= 14.3029 E= 1.5e-030 -1089 260 -1089 -1089 157 -1089 -1089 -1089 157 -1089 -1089 -1089 157 -1089 -1089 -1089 157 -1089 -1089 -1089 -1089 260 -1089 -1089 -1089 -1089 -1089 157 -1089 -1089 -1089 157 157 -1089 -1089 -1089 -1089 -1089 -1089 157 157 -1089 -1089 -1089 -1089 -1089 -1089 157 157 -1089 -1089 -1089 157 -1089 -1089 -1089 -1089 260 -1089 -1089 157 -1089 -1089 -1089 -1089 260 -1089 -1089 157 -1089 -1089 -1089 -1089 -1089 260 -1089 157 -1089 -1089 -1089 -267 -1089 253 -1089 157 -1089 -1089 -1089 -1089 -1089 -1089 157 -1089 -1089 -1089 157 -267 -1089 -1089 150 -1089 -1089 253 -267 157 -1089 -1089 -1089 -1089 -1089 -1089 157 157 -1089 -1089 -1089 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAAACTTATATAACACAGAGATTTGATA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 19 E= 1.5e-030 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 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 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 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 1.000000 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 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.052632 0.000000 0.947368 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 0.052632 0.000000 0.000000 0.947368 0.000000 0.000000 0.947368 0.052632 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CAAAACTTATATAACACAGAGATTTGATA MEME-2 regular expression -------------------------------------------------------------------------------- CAAAACTTATATAACACAGAGATTTGATA -------------------------------------------------------------------------------- Time 227.27 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************