******************************************************************************** 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/AT3G50060_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/AT3G50060_peak_sequences.fasta -dna -oc out/AT3G50060 -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= 3207 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= 649340 N= 3207 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.336 C 0.164 G 0.164 T 0.336 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 DAAHHWAACCGWWWH MEME-1 width = 15 sites = 3197 llr = 22201 E-value = 3.6e-197 ******************************************************************************** -------------------------------------------------------------------------------- Motif DAAHHWAACCGWWWH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 455444aa::13554 pos.-specific C 212332::a5:1212 probability G 22111::::291:1: matrix T 222324:::3:5333 bits 2.6 * 2.4 * 2.1 * * 1.8 * * Relative 1.6 *** * Entropy 1.3 *** * (10.0 bits) 1.0 *** * 0.8 ***** 0.5 ***** 0.3 *** ***** ** 0.0 --------------- Multilevel AAAAAAAACCGTAAA consensus GTTCCT T ATTT sequence T TT G C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAAHHWAACCGWWWH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 604442 bayes= 9.48179 E= 3.6e-197 30 -7 42 -66 66 -126 20 -67 67 20 -113 -74 21 81 -147 -34 24 80 -78 -60 25 10 -183 17 156 -557 -1829 -807 157 -1829 -1829 -1829 -1829 261 -1829 -1829 -807 170 34 -38 -194 -803 248 -1007 -10 -70 -78 55 42 42 -903 -3 67 -95 -108 -15 17 50 -181 3 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAAHHWAACCGWWWH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3197 E= 3.6e-197 0.413825 0.155458 0.218330 0.212387 0.533000 0.068189 0.187676 0.211135 0.536753 0.187676 0.074758 0.200813 0.389428 0.286206 0.059118 0.265249 0.397873 0.284955 0.095402 0.221770 0.400688 0.175790 0.045981 0.377541 0.995308 0.003441 0.000000 0.001251 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.001251 0.532687 0.207695 0.258367 0.087582 0.000626 0.911480 0.000313 0.312793 0.100719 0.095402 0.491085 0.450735 0.218642 0.000313 0.330310 0.535502 0.084767 0.077260 0.302471 0.377854 0.231467 0.046606 0.344073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DAAHHWAACCGWWWH MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][AT][AT][ACT][ACT][AT]AAC[CTG]G[TA][ATC][AT][ATC] -------------------------------------------------------------------------------- Time 71.79 secs. ******************************************************************************** ******************************************************************************** MOTIF YGGTTYGGTTYGGTT MEME-2 width = 15 sites = 291 llr = 3405 E-value = 1.6e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif YGGTTYGGTTYGGTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :1:::112:::11:1 pos.-specific C 31:::3::116:::: probability G 267:12761::991: matrix T 413a9412894::99 bits 2.6 2.4 2.1 ** 1.8 ** Relative 1.6 * ** Entropy 1.3 * * **** (16.9 bits) 1.0 *** * ***** 0.8 **** ********* 0.5 ***** ********* 0.3 *************** 0.0 --------------- Multilevel TGGTTTGGTTCGGTT consensus C T C T T sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGTTYGGTTYGGTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 604442 bayes= 13.0553 E= 1.6e-010 -1483 109 33 41 -122 -118 197 -126 -403 -325 200 -12 -1483 -1483 -1483 157 -1483 -187 -140 141 -236 95 13 39 -133 -1483 216 -133 -106 -1483 186 -46 -291 -111 -140 128 -1483 -53 -1483 140 -1483 189 -1483 23 -181 -1483 247 -1483 -222 -1483 250 -1483 -381 -257 -125 139 -215 -277 -257 138 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGTTYGGTTYGGTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 291 E= 1.6e-010 0.000000 0.347079 0.206186 0.446735 0.144330 0.072165 0.642612 0.140893 0.020619 0.017182 0.652921 0.309278 0.000000 0.000000 0.000000 1.000000 0.000000 0.044674 0.061856 0.893471 0.065292 0.316151 0.178694 0.439863 0.134021 0.000000 0.731959 0.134021 0.161512 0.000000 0.594502 0.243986 0.044674 0.075601 0.061856 0.817869 0.000000 0.113402 0.000000 0.886598 0.000000 0.604811 0.000000 0.395189 0.096220 0.000000 0.903780 0.000000 0.072165 0.000000 0.927835 0.000000 0.024055 0.027491 0.068729 0.879725 0.075601 0.024055 0.027491 0.872852 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YGGTTYGGTTYGGTT MEME-2 regular expression -------------------------------------------------------------------------------- [TCG]G[GT]TT[TC]G[GT]TT[CT]GGTT -------------------------------------------------------------------------------- Time 133.50 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************