******************************************************************************** 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/AT3G30210_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/AT3G30210_peak_sequences.fasta -dna -oc out/AT3G30210 -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= 2347 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= 365956 N= 2347 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.335 C 0.165 G 0.165 T 0.335 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 DDDWWWWGTTAGGTAN MEME-1 width = 16 sites = 2271 llr = 19668 E-value = 4.0e-776 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDDWWWWGTTAGGTAN MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34444552::a:::63 pos.-specific C 211111:::::::122 probability G 222222183::aa:12 matrix T 3333333:7a:::913 bits 2.6 ** 2.3 ** 2.1 ** 1.8 ** Relative 1.6 * * ** Entropy 1.3 * ***** (12.5 bits) 1.0 ******* 0.8 ******* 0.5 ******* 0.3 ********* 0.0 ---------------- Multilevel AAAAAAAGTTAGGTAA consensus TTTTTTTAG T sequence G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDWWWWGTTAGGTAN MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 330751 bayes= 8.96837 E= 4.0e-776 3 -6 12 -6 9 -40 31 -10 19 -42 24 -16 30 -41 0 -17 31 -97 5 -3 49 -158 -1 -12 69 -243 -23 -23 -70 -1779 222 -353 -1779 -1779 88 106 -1779 -1779 -1779 157 151 -495 -1779 -331 -1779 -1779 261 -1779 -1779 -1779 261 -1779 -1779 -93 -1779 144 83 2 -57 -144 -2 30 3 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDWWWWGTTAGGTAN MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 2271 E= 4.0e-776 0.343021 0.156759 0.177455 0.322765 0.358873 0.123734 0.202994 0.314399 0.383972 0.122413 0.193307 0.300308 0.415236 0.122853 0.163804 0.298107 0.416997 0.083664 0.169969 0.329370 0.473800 0.054601 0.162483 0.309115 0.544254 0.030383 0.139146 0.286218 0.207398 0.000000 0.763540 0.029062 0.000000 0.000000 0.301189 0.698811 0.000000 0.000000 0.000000 1.000000 0.960810 0.005284 0.000000 0.033906 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.085865 0.000000 0.914135 0.599736 0.166006 0.110084 0.124174 0.332453 0.202114 0.167327 0.298107 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDWWWWGTTAGGTAN MEME-1 regular expression -------------------------------------------------------------------------------- [AT][ATG][AT][AT][AT][AT][AT][GA][TG]TAGGTA[ATC] -------------------------------------------------------------------------------- Time 71.34 secs. ******************************************************************************** ******************************************************************************** MOTIF TCGGTTTGGTTTKGTTYGGT MEME-2 width = 20 sites = 52 llr = 741 E-value = 6.6e-009 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCGGTTTGGTTTKGTTYGGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 11:1::::11::::::1112 pos.-specific C 161:::31::1221::42:1 probability G 12882::682::572:1791 matrix T 72118a73179732894:17 bits 2.6 2.3 2.1 1.8 * Relative 1.6 ** * * * Entropy 1.3 ** * * * ** (20.6 bits) 1.0 ******* * * * ** 0.8 ********** *** ** 0.5 ******************* 0.3 ******************** 0.0 -------------------- Multilevel TCGGTTTGGTTTGGTTCGGT consensus T CT G CT G T sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGGTTTGGTTTKGTTYGGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 321363 bayes= 14.5282 E= 6.6e-009 -132 -150 -50 104 -213 177 -9 -67 -313 -150 230 -181 -213 -1234 234 -181 -1234 -1234 23 126 -1234 -1234 -309 154 -1234 82 -1234 108 -1234 -77 191 -22 -254 -1234 237 -181 -254 -1234 50 108 -1234 -77 -209 136 -313 50 -209 104 -313 37 155 -32 -1234 -77 216 -96 -313 -1234 37 116 -313 -1234 -209 146 -181 143 -109 19 -132 -9 212 -1234 -254 -1234 240 -213 -113 -77 -77 96 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGGTTTGGTTTKGTTYGGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 52 E= 6.6e-009 0.134615 0.057692 0.115385 0.692308 0.076923 0.557692 0.153846 0.211538 0.038462 0.057692 0.807692 0.096154 0.076923 0.000000 0.826923 0.096154 0.000000 0.000000 0.192308 0.807692 0.000000 0.000000 0.019231 0.980769 0.000000 0.288462 0.000000 0.711538 0.000000 0.096154 0.615385 0.288462 0.057692 0.000000 0.846154 0.096154 0.057692 0.000000 0.230769 0.711538 0.000000 0.096154 0.038462 0.865385 0.038462 0.230769 0.038462 0.692308 0.038462 0.211538 0.480769 0.269231 0.000000 0.096154 0.730769 0.173077 0.038462 0.000000 0.211538 0.750000 0.038462 0.000000 0.038462 0.923077 0.096154 0.442308 0.076923 0.384615 0.134615 0.153846 0.711538 0.000000 0.057692 0.000000 0.865385 0.076923 0.153846 0.096154 0.096154 0.653846 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCGGTTTGGTTTKGTTYGGT MEME-2 regular expression -------------------------------------------------------------------------------- T[CT]GGTT[TC][GT]G[TG]T[TC][GTC]G[TG]T[CT]GGT -------------------------------------------------------------------------------- Time 130.94 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************