******************************************************************************** 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/AT1G75390_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/AT1G75390_peak_sequences.fasta -dna -oc out/AT1G75390 -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= 2718 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= 372968 N= 2718 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.294 C 0.206 G 0.206 T 0.294 Background letter frequencies (from file dataset with add-one prior applied): A 0.296 C 0.204 G 0.204 T 0.296 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDWGVTSACGTGGCA MEME-1 width = 15 sites = 2324 llr = 23300 E-value = 6.2e-1031 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDWGVTSACGTGGCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 343232:a:::::25 pos.-specific C 111:323:9::::81 probability G 32152:6::a:a7:2 matrix T 3342261:1:a:3:2 bits 2.3 * * 2.1 * * 1.8 ***** 1.6 ***** Relative 1.4 ***** Entropy 1.1 ******* (14.5 bits) 0.9 ******* 0.7 ******** 0.5 * ********* 0.2 * ********** 0.0 --------------- Multilevel AATGCTGACGTGGCA consensus TTATACC TA sequence GG G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDWGVTSACGTGGCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 334916 bayes= 9.45172 E= 6.2e-1031 18 -102 44 -5 26 -49 0 1 8 -68 -49 49 -80 -219 142 -31 -19 69 29 -86 -66 12 -1783 100 -543 65 143 -126 175 -1783 -1783 -1783 -1783 221 -498 -252 -457 -789 228 -1783 -1783 -1783 -1783 175 -662 -1783 229 -710 -543 -1783 179 -3 -56 189 -413 -316 89 -74 -20 -97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDWGVTSACGTGGCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2324 E= 6.2e-1031 0.336059 0.100688 0.276678 0.286575 0.353701 0.145009 0.203528 0.297762 0.312392 0.127367 0.144578 0.415663 0.170396 0.044750 0.546041 0.238812 0.259466 0.328744 0.248279 0.163511 0.188038 0.221170 0.000000 0.590792 0.006885 0.318847 0.550344 0.123924 1.000000 0.000000 0.000000 0.000000 0.000000 0.941910 0.006454 0.051635 0.012478 0.000861 0.986661 0.000000 0.000000 0.000000 0.000000 1.000000 0.003012 0.000000 0.994836 0.002151 0.006885 0.000000 0.702668 0.290448 0.200947 0.754303 0.011618 0.033133 0.549484 0.122203 0.177281 0.151033 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDWGVTSACGTGGCA MEME-1 regular expression -------------------------------------------------------------------------------- [ATG][ATG][TA][GT][CAG][TC][GC]ACGTG[GT][CA]A -------------------------------------------------------------------------------- Time 128.09 secs. ******************************************************************************** ******************************************************************************** MOTIF TATATATGAAAGDWGGCYAACTCTCTCCM MEME-2 width = 29 sites = 20 llr = 622 E-value = 5.1e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif TATATATGAAAGDWGGCYAACTCTCTCCM MEME-2 Description -------------------------------------------------------------------------------- Simplified A :a:a:a::aaa136:211aa:1::::1:4 pos.-specific C ::::::11:::::::174::9:a:a:8a6 probability G :::::::9:::a3:a7::::1:::::::: matrix T a:a1a:9:::::55:136::191a1a2:: bits 2.3 * * 2.1 * * * * * 1.8 *** ** ***** * ** **** * 1.6 *** ** ***** * *** **** * Relative 1.4 ************ * ******** * Entropy 1.1 ************ * *********** (44.9 bits) 0.9 ************ * * *********** 0.7 ************ **************** 0.5 ***************************** 0.2 ***************************** 0.0 ----------------------------- Multilevel TATATATGAAAGTAGGCTAACTCTCTCCC consensus AT ATC T A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATATATGAAAGDWGGCYAACTCTCTCCM MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 296864 bayes= 14.109 E= 5.1e-038 -1097 -1097 -1097 175 175 -1097 -1097 -1097 -1097 -1097 -1097 175 168 -1097 -1097 -256 -1097 -1097 -1097 175 175 -1097 -1097 -1097 -1097 -103 -1097 160 -1097 -103 214 -1097 175 -1097 -1097 -1097 175 -1097 -1097 -1097 175 -1097 -1097 -1097 -256 -1097 222 -1097 2 -1097 30 60 89 -1097 -1097 60 -1097 -1097 229 -1097 -57 -103 167 -256 -256 167 -1097 2 -256 97 -1097 89 175 -1097 -1097 -1097 175 -1097 -1097 -1097 -1097 206 -103 -256 -157 -1097 -1097 160 -1097 222 -1097 -256 -1097 -1097 -1097 175 -1097 222 -1097 -256 -1097 -1097 -1097 175 -256 188 -1097 -57 -1097 229 -1097 -1097 43 156 -1097 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATATATGAAAGDWGGCYAACTCTCTCCM MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 20 E= 5.1e-038 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.950000 0.000000 0.000000 0.050000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.100000 0.000000 0.900000 0.000000 0.100000 0.900000 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 0.050000 0.000000 0.950000 0.000000 0.300000 0.000000 0.250000 0.450000 0.550000 0.000000 0.000000 0.450000 0.000000 0.000000 1.000000 0.000000 0.200000 0.100000 0.650000 0.050000 0.050000 0.650000 0.000000 0.300000 0.050000 0.400000 0.000000 0.550000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.850000 0.100000 0.050000 0.100000 0.000000 0.000000 0.900000 0.000000 0.950000 0.000000 0.050000 0.000000 0.000000 0.000000 1.000000 0.000000 0.950000 0.000000 0.050000 0.000000 0.000000 0.000000 1.000000 0.050000 0.750000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TATATATGAAAGDWGGCYAACTCTCTCCM MEME-2 regular expression -------------------------------------------------------------------------------- TATATATGAAAG[TAG][AT]G[GA][CT][TC]AACTCTCT[CT]C[CA] -------------------------------------------------------------------------------- Time 231.33 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************