******************************************************************************** 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/AT5G39610_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/AT5G39610_peak_sequences.fasta -dna -oc out/AT5G39610 -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= 3838 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= 929249 N= 3838 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.313 C 0.187 G 0.187 T 0.313 Background letter frequencies (from file dataset with add-one prior applied): A 0.314 C 0.186 G 0.186 T 0.314 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTRCKTGTDNDWBAA MEME-1 width = 15 sites = 3807 llr = 27008 E-value = 1.8e-164 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTRCKTGTDNDWBAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A :24:::113344275 pos.-specific C ::1a::1122213:3 probability G :24:6:813322211 matrix T 962:4a:63223221 bits 2.4 2.2 * 1.9 * 1.7 * ** Relative 1.5 * * ** Entropy 1.2 * **** (10.2 bits) 1.0 * **** 0.7 * **** 0.5 ** **** * 0.2 ******** *** 0.0 --------------- Multilevel TTACGTGTAGAACAA consensus GG T GAGTT C sequence TTT G C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTRCKTGTDNDWBAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 875517 bayes= 9.63179 E= 1.8e-164 -268 -1854 -614 159 -90 -522 20 96 31 -134 101 -94 -439 240 -1854 -705 -1854 -1854 175 26 -1854 -1854 -666 167 -159 -183 218 -1854 -110 -71 -83 101 4 -29 55 -30 -21 19 71 -56 20 -8 34 -46 46 -92 -4 -12 -87 90 32 -34 114 -194 -133 -75 77 53 -53 -220 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTRCKTGTDNDWBAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3807 E= 1.8e-164 0.049120 0.000000 0.002627 0.948253 0.168374 0.004991 0.213554 0.613081 0.390071 0.073286 0.372997 0.163646 0.014972 0.982664 0.000000 0.002364 0.000000 0.000000 0.623325 0.376675 0.000000 0.000000 0.001839 0.998161 0.104282 0.052272 0.843446 0.000000 0.147097 0.113738 0.104282 0.634883 0.323352 0.151300 0.270817 0.254531 0.272130 0.211190 0.303126 0.213554 0.361177 0.175729 0.234831 0.228264 0.432099 0.098240 0.180194 0.289467 0.172314 0.347518 0.231416 0.248752 0.690570 0.048332 0.073811 0.187287 0.535592 0.267665 0.128448 0.068295 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTRCKTGTDNDWBAA MEME-1 regular expression -------------------------------------------------------------------------------- T[TG][AG]C[GT]TGT[AGT][GATC][AGT][AT][CTG]A[AC] -------------------------------------------------------------------------------- Time 69.11 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARAARAARAARAARAARAB MEME-2 width = 21 sites = 943 llr = 9547 E-value = 1.4e-040 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAB MEME-2 Description -------------------------------------------------------------------------------- Simplified A 556578496669497668671 pos.-specific C 2111111:1:11111111::3 probability G 32132:51332:5:2321414 matrix T :12::1::::::::1:1::23 bits 2.4 2.2 1.9 1.7 Relative 1.5 * Entropy 1.2 * * * (14.6 bits) 1.0 * * * * * 0.7 **** * *** * *** 0.5 * ************* *** 0.2 ********************* 0.0 --------------------- Multilevel AAAAAAGAAAAAGAAAAAAAG consensus G G A GGG A GG GTT sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAB MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 852489 bayes= 12.0937 E= 1.4e-040 56 13 85 -1652 78 -63 10 -113 99 -117 -41 -105 62 -37 89 -340 117 -70 -7 -1652 142 -111 -1652 -208 36 -120 143 -440 158 -1652 -164 -1652 105 -181 49 -304 97 -199 84 -663 102 -57 13 -326 152 -94 -1652 -1652 48 -113 136 -1652 152 -187 -206 -1652 108 -139 -7 -182 89 -167 86 -389 90 -78 30 -200 137 -124 -126 -321 81 -1652 127 -1652 122 -745 -152 -63 -208 47 98 -6 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAB MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 943 E= 1.4e-040 0.462354 0.203606 0.334040 0.000000 0.538706 0.119830 0.198303 0.143160 0.625663 0.082715 0.139979 0.151644 0.482503 0.143160 0.344645 0.029692 0.708378 0.114528 0.177094 0.000000 0.839873 0.085896 0.000000 0.074231 0.402969 0.080594 0.501591 0.014846 0.940615 0.000000 0.059385 0.000000 0.648993 0.053022 0.259809 0.038176 0.617179 0.046660 0.332980 0.003181 0.638388 0.125133 0.203606 0.032874 0.903499 0.096501 0.000000 0.000000 0.437964 0.084836 0.477200 0.000000 0.904560 0.050901 0.044539 0.000000 0.662778 0.071050 0.177094 0.089077 0.583245 0.058324 0.337222 0.021209 0.585366 0.108165 0.227996 0.078473 0.810180 0.078473 0.077413 0.033934 0.552492 0.000000 0.447508 0.000000 0.731707 0.001060 0.064687 0.202545 0.074231 0.256628 0.366914 0.302227 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARAARAB MEME-2 regular expression -------------------------------------------------------------------------------- [AGC]AA[AG]AA[GA]A[AG][AG][AG]A[GA]AA[AG][AG]A[AG][AT][GTC] -------------------------------------------------------------------------------- Time 130.68 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************