******************************************************************************** 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/AT5G17800_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/AT5G17800_peak_sequences.fasta -dna -oc out/AT5G17800 -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= 1982 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= 330789 N= 1982 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 0.335 C 0.165 G 0.165 T 0.335 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WWDWCCGTTAW MEME-1 width = 11 sites = 1958 llr = 14721 E-value = 3.0e-422 ******************************************************************************** -------------------------------------------------------------------------------- Motif WWDWCCGTTAW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5646:2:::a3 pos.-specific C 1:::78::::1 probability G 2131::a:::1 matrix T 33443::aa:5 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.6 * *** Entropy 1.3 ****** (10.8 bits) 1.0 ****** 0.8 ****** 0.5 ****** 0.3 ********* 0.0 ----------- Multilevel AATACCGTTAT consensus TTATT A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDWCCGTTAW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 310969 bayes= 8.59667 E= 3.0e-422 43 -79 27 -41 73 -248 -60 -13 12 -375 61 15 75 -1758 -98 8 -1758 218 -675 -42 -110 224 -250 -311 -1758 -1758 260 -1758 -1758 -1758 -487 157 -1758 -1758 -1758 158 152 -1758 -258 -477 -13 -68 -26 44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDWCCGTTAW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1958 E= 3.0e-422 0.453013 0.095506 0.198672 0.252809 0.555669 0.029622 0.108784 0.305924 0.363636 0.012257 0.251277 0.372829 0.562308 0.000000 0.083759 0.353933 0.000000 0.747702 0.001532 0.250766 0.156282 0.775792 0.029111 0.038815 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.005618 0.994382 0.000000 0.000000 0.000000 1.000000 0.960163 0.000000 0.027579 0.012257 0.305924 0.102656 0.137385 0.454035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WWDWCCGTTAW MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][TAG][AT][CT]CGTTA[TA] -------------------------------------------------------------------------------- Time 72.09 secs. ******************************************************************************** ******************************************************************************** MOTIF ATAACGGCATGTCTATTTTGGCCTGGTCAACGAAWRATCATGTT MEME-2 width = 44 sites = 16 llr = 736 E-value = 7.1e-044 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATAACGGCATGTCTATTTTGGCCTGGTCAACGAAWRATCATGTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 9:a9:13:9:::1:9111:1::1111::9a:1a9568118::1: pos.-specific C ::::a::a::::9::1::1::881:::9::a::::11:7:2::: probability G :::1:96:1:a1111::::9a11:99::1::9:::4:::1:9:1 matrix T 1a::::1::a:9:919999::1:9::a1:::::15:19318199 bits 2.6 * * * * * 2.3 * * * * * 2.1 ** * * ** * * ** 1.8 ** * * * ** ** * ** * Relative 1.6 ** ** * ** * **** **** **** * Entropy 1.3 ***** **** * ***** ********* ** (66.4 bits) 1.0 ********************************** ** **** 0.8 ********************************** * ******* 0.5 ******************************************** 0.3 ******************************************** 0.0 -------------------------------------------- Multilevel ATAACGGCATGTCTATTTTGGCCTGGTCAACGAAAAATCATGTT consensus A TG T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATAACGGCATGTCTATTTTGGCCTGGTCAACGAAWRATCATGTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 44 n= 245563 bayes= 13.9056 E= 7.1e-044 138 -1064 -1064 -142 -1064 -1064 -1064 158 158 -1064 -1064 -1064 148 -1064 -140 -1064 -1064 260 -1064 -1064 -242 -1064 251 -1064 -42 -1064 192 -142 -1064 260 -1064 -1064 148 -1064 -140 -1064 -1064 -1064 -1064 158 -1064 -1064 260 -1064 -1064 -1064 -40 138 -242 241 -140 -1064 -1064 -1064 -40 138 138 -1064 -140 -242 -242 -140 -1064 138 -142 -1064 -1064 138 -142 -1064 -1064 138 -1064 -140 -1064 148 -242 -1064 251 -1064 -1064 -1064 260 -1064 -1064 230 -140 -142 -142 230 -140 -1064 -242 -140 -1064 138 -142 -1064 241 -1064 -242 -1064 251 -1064 -1064 -1064 -1064 158 -1064 251 -1064 -242 148 -1064 -140 -1064 158 -1064 -1064 -1064 -1064 260 -1064 -1064 -242 -1064 251 -1064 158 -1064 -1064 -1064 138 -1064 -1064 -142 58 -1064 -1064 58 75 -140 119 -1064 116 -40 -1064 -142 -142 -1064 -1064 138 -242 206 -1064 -42 128 -1064 -140 -142 -1064 19 -1064 128 -1064 -1064 241 -142 -242 -1064 -1064 148 -1064 -1064 -40 138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATAACGGCATGTCTATTTTGGCCTGGTCAACGAAWRATCATGTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 44 nsites= 16 E= 7.1e-044 0.875000 0.000000 0.000000 0.125000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.937500 0.000000 0.062500 0.000000 0.000000 1.000000 0.000000 0.000000 0.062500 0.000000 0.937500 0.000000 0.250000 0.000000 0.625000 0.125000 0.000000 1.000000 0.000000 0.000000 0.937500 0.000000 0.062500 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.062500 0.875000 0.062500 0.000000 0.000000 0.000000 0.125000 0.875000 0.875000 0.000000 0.062500 0.062500 0.062500 0.062500 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.875000 0.000000 0.062500 0.000000 0.937500 0.062500 0.000000 0.937500 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.812500 0.062500 0.125000 0.125000 0.812500 0.062500 0.000000 0.062500 0.062500 0.000000 0.875000 0.125000 0.000000 0.875000 0.000000 0.062500 0.000000 0.937500 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.937500 0.000000 0.062500 0.937500 0.000000 0.062500 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.062500 0.000000 0.937500 0.000000 1.000000 0.000000 0.000000 0.000000 0.875000 0.000000 0.000000 0.125000 0.500000 0.000000 0.000000 0.500000 0.562500 0.062500 0.375000 0.000000 0.750000 0.125000 0.000000 0.125000 0.125000 0.000000 0.000000 0.875000 0.062500 0.687500 0.000000 0.250000 0.812500 0.000000 0.062500 0.125000 0.000000 0.187500 0.000000 0.812500 0.000000 0.000000 0.875000 0.125000 0.062500 0.000000 0.000000 0.937500 0.000000 0.000000 0.125000 0.875000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATAACGGCATGTCTATTTTGGCCTGGTCAACGAAWRATCATGTT MEME-2 regular expression -------------------------------------------------------------------------------- ATAACG[GA]CATGTCTATTTTGGCCTGGTCAACGAA[AT][AG]AT[CT]ATGTT -------------------------------------------------------------------------------- Time 132.01 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************