******************************************************************************** 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/AT1G69490_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/AT1G69490_peak_sequences.fasta -dna -oc out/AT1G69490 -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= 2352 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= 326509 N= 2352 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.322 C 0.178 G 0.178 T 0.322 Background letter frequencies (from file dataset with add-one prior applied): A 0.323 C 0.177 G 0.177 T 0.323 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF ARRTTACGTRTNNDW MEME-1 width = 15 sites = 2347 llr = 16444 E-value = 3.3e-409 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARRTTACGTRTNNDW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 553215:::324345 pos.-specific C 211::2a::112211 probability G 135:32:a:512221 matrix T 211861::a:62233 bits 2.5 ** 2.3 ** 2.0 ** 1.8 ** Relative 1.5 *** Entropy 1.3 *** (10.1 bits) 1.0 *** 0.8 ** **** 0.5 *** **** 0.3 ********** 0.0 --------------- Multilevel AAGTTACGTGTAAAA consensus TGAAGG AATTTT sequence GG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARRTTACGTRTNNDW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 293581 bayes= 8.10861 E= 3.3e-409 56 10 -63 -56 51 -101 96 -157 -21 -117 152 -125 -48 -1784 -669 124 -229 -552 76 96 67 2 40 -216 -698 248 -479 -676 -1784 -1784 249 -525 -1784 -869 -711 163 -16 -32 159 -318 -39 -58 -150 82 15 17 16 -40 8 3 39 -39 32 -39 23 -35 65 -104 -56 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARRTTACGTRTNNDW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2347 E= 3.3e-409 0.477631 0.189178 0.114188 0.219003 0.460588 0.087772 0.342565 0.109075 0.280358 0.078398 0.505326 0.135918 0.232211 0.000000 0.001704 0.766084 0.066042 0.003835 0.299531 0.630592 0.514700 0.179378 0.233490 0.072433 0.002556 0.988070 0.006391 0.002983 0.000000 0.000000 0.991478 0.008522 0.000000 0.000426 0.001278 0.998296 0.289732 0.141457 0.533021 0.035790 0.246272 0.118449 0.062633 0.572646 0.358330 0.198977 0.197273 0.245420 0.341713 0.179804 0.231359 0.247124 0.404772 0.135066 0.207073 0.253089 0.507030 0.085641 0.120153 0.287175 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARRTTACGTRTNNDW MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AG][GA][TA][TG][AG]CGT[GA][TA][AT][ATG][ATG][AT] -------------------------------------------------------------------------------- Time 133.23 secs. ******************************************************************************** ******************************************************************************** MOTIF KCDGAGGACYTNGTCANRAACAACTYGGTGAAATMTKGACGGCCAAGCAT MEME-2 width = 50 sites = 5 llr = 265 E-value = 1.2e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif KCDGAGGACYTNGTCANRAACAACTYGGTGAAATMTKGACGGCCAAGCAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :22:a::a:::2::2a44aa:aa::::::2aaa:4:::a2:::28a::a: pos.-specific C :8::::::a6:2::6:2:::8::a262:::::::6::::6::66:::6:: probability G 6:4a:8a::::48:::26::::::::8a:8::::::4a::8a2:2:a2:: matrix T 4:4::2:::4a22a2:2:::2:::84::a::::a:a6::22:22:::2:a bits 2.5 * * * * * * * * 2.3 * * * * * * * * 2.0 * * * * * * * * 1.8 ** *** * * * ** *** *** **** * ** * ** ** Relative 1.5 * ****** * ** * ****** ******** * ** ** ** ** Entropy 1.3 ** ******** ** * ******* *********** ** ** ** ** (76.4 bits) 1.0 ** ******** ** * ********************** *** ****** 0.8 ** ******** **** ********************************* 0.5 *********** **** ********************************* 0.3 **************** ********************************* 0.0 -------------------------------------------------- Multilevel GCGGAGGACCTGGTCAAGAACAACTCGGTGAAATCTTGACGGCCAAGCAT consensus TAT T T AT A CA T CTC A A G AT GAG G sequence A C T G T TT T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDGAGGACYTNGTCANRAACAACTYGGTGAAATMTKGACGGCCAAGCAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 211261 bayes= 15.6182 E= 1.2e-002 -897 -897 176 31 -69 218 -897 -897 -69 -897 118 31 -897 -897 250 -897 163 -897 -897 -897 -897 -897 218 -69 -897 -897 250 -897 163 -897 -897 -897 -897 250 -897 -897 -897 176 -897 31 -897 -897 -897 163 -69 18 118 -69 -897 -897 218 -69 -897 -897 -897 163 -69 176 -897 -69 163 -897 -897 -897 31 18 18 -69 31 -897 176 -897 163 -897 -897 -897 163 -897 -897 -897 -897 218 -897 -69 163 -897 -897 -897 163 -897 -897 -897 -897 250 -897 -897 -897 18 -897 130 -897 176 -897 31 -897 18 218 -897 -897 -897 250 -897 -897 -897 -897 163 -69 -897 218 -897 163 -897 -897 -897 163 -897 -897 -897 163 -897 -897 -897 -897 -897 -897 163 31 176 -897 -897 -897 -897 -897 163 -897 -897 118 89 -897 -897 250 -897 163 -897 -897 -897 -69 176 -897 -69 -897 -897 218 -69 -897 -897 250 -897 -897 176 18 -69 -69 176 -897 -69 130 -897 18 -897 163 -897 -897 -897 -897 -897 250 -897 -897 176 18 -69 163 -897 -897 -897 -897 -897 -897 163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDGAGGACYTNGTCANRAACAACTYGGTGAAATMTKGACGGCCAAGCAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 5 E= 1.2e-002 0.000000 0.000000 0.600000 0.400000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.400000 0.400000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.600000 0.000000 0.400000 0.000000 0.000000 0.000000 1.000000 0.200000 0.200000 0.400000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 0.000000 1.000000 0.200000 0.600000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.400000 0.000000 0.600000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.000000 0.200000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.600000 0.000000 0.400000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.200000 0.000000 0.800000 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 0.000000 0.000000 0.000000 1.000000 0.400000 0.600000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.600000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.600000 0.000000 0.200000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.200000 0.200000 0.200000 0.600000 0.000000 0.200000 0.800000 0.000000 0.200000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.600000 0.200000 0.200000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif KCDGAGGACYTNGTCANRAACAACTYGGTGAAATMTKGACGGCCAAGCAT MEME-2 regular expression -------------------------------------------------------------------------------- [GT][CA][GTA]GA[GT]GAC[CT]T[GACT][GT]T[CAT]A[ACGT][GA]AA[CT]AAC[TC][CT][GC]GT[GA]AAAT[CA]T[TG]GA[CAT][GT]G[CGT][CAT][AG]AG[CGT]AT -------------------------------------------------------------------------------- Time 236.94 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************