******************************************************************************** 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/AT1G03800_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/AT1G03800_peak_sequences.fasta -dna -oc out/AT1G03800 -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= 4780 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= 1108213 N= 4780 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 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 0.257 C 0.243 G 0.243 T 0.257 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NHHDYCGCCGCCRYHDHHNHH MEME-1 width = 21 sites = 4760 llr = 42902 E-value = 2.8e-475 ******************************************************************************** -------------------------------------------------------------------------------- Motif NHHDYCGCCGCCRYHDHHNHH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3223121:::1:323332222 pos.-specific C 234148:aa:8a:33134234 probability G 21121:9::a::511311311 matrix T 33343:1:::2:143333333 bits 2.0 ** 1.8 *** * 1.6 *** * 1.4 *** * Relative 1.2 ***** * Entropy 1.0 ******* (13.0 bits) 0.8 ******* 0.6 ******** 0.4 ******** 0.2 ** ********** * * 0.0 --------------------- Multilevel TCCTCCGCCGCCGTTATCGCC consensus ATTAT ACCTCTTTT sequence GAAG AGAAAAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHHDYCGCCGCCRYHDHHNHH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1012613 bayes= 9.60885 E= 2.8e-475 18 -48 -16 30 -33 52 -101 35 -12 76 -181 13 11 -87 -10 50 -133 83 -90 38 -71 175 -418 -483 -228 -701 181 -152 -1886 200 -330 -793 -635 203 -859 -1886 -567 -659 202 -655 -227 165 -403 -60 -251 197 -1886 -635 42 -401 110 -109 -66 48 -121 61 11 20 -103 33 38 -128 12 24 -1 31 -117 39 -18 63 -143 26 -5 -49 31 11 -25 43 -76 28 -28 78 -106 -1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHHDYCGCCGCCRYHDHHNHH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4760 E= 2.8e-475 0.291387 0.174580 0.217857 0.316176 0.204622 0.347899 0.121008 0.326471 0.236765 0.413025 0.069328 0.280882 0.277311 0.132773 0.226471 0.363445 0.102101 0.434034 0.130462 0.333403 0.156933 0.820588 0.013445 0.009034 0.052941 0.001891 0.855882 0.089286 0.000000 0.974160 0.024790 0.001050 0.003151 0.996218 0.000630 0.000000 0.005042 0.002521 0.989706 0.002731 0.053361 0.762185 0.014916 0.169538 0.045168 0.951681 0.000000 0.003151 0.343908 0.015126 0.520798 0.120168 0.162395 0.339916 0.105252 0.392437 0.277731 0.280462 0.119118 0.322689 0.332773 0.100000 0.264496 0.302731 0.255672 0.301050 0.107983 0.335294 0.225840 0.377521 0.090126 0.306513 0.247899 0.173529 0.302521 0.276050 0.215336 0.328782 0.144118 0.311765 0.211555 0.416597 0.116807 0.255042 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHHDYCGCCGCCRYHDHHNHH MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][CTA][CTA][TAG][CT]CGCCGCC[GA][TC][TCA][ATG][TCA][CTA][GTA][CTA][CTA] -------------------------------------------------------------------------------- Time 152.00 secs. ******************************************************************************** ******************************************************************************** Stopped because MEME would probably exceed the allowed time (300.00 secs) before finding the next motif. ******************************************************************************** CPU: nid004083 ********************************************************************************