******************************************************************************** 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/AT5G10030_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/AT5G10030_peak_sequences.fasta -dna -oc out/AT5G10030 -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= 6121 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= 1322155 N= 6121 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.311 C 0.189 G 0.189 T 0.311 Background letter frequencies (from file dataset with add-one prior applied): A 0.313 C 0.187 G 0.187 T 0.313 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DWWGATGACGTVDNH MEME-1 width = 15 sites = 6091 llr = 49069 E-value = 3.5e-394 ******************************************************************************** -------------------------------------------------------------------------------- Motif DWWGATGACGTVDNH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34326::a:113423 pos.-specific C 11212:::8::3:33 probability G 32162:9::9:3321 matrix T 2341:a1:2:81233 bits 2.4 2.2 1.9 * * 1.7 ***** Relative 1.4 ***** Entropy 1.2 ***** (11.6 bits) 1.0 ***** 0.7 ****** 0.5 ******** 0.2 ********** 0.0 --------------- Multilevel AATGATGACGTCACA consensus GTA G AGTC sequence T C GTAT G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWWGATGACGTVDNH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1236461 bayes= 9.92637 E= 3.5e-394 13 -73 67 -35 40 -73 -8 -7 -17 -27 -37 43 -79 -104 166 -120 83 21 24 -572 -809 -783 -1922 167 -1089 -1922 227 -175 168 -1922 -1922 -857 -989 218 -916 -104 -260 -607 233 -857 -140 -212 -362 140 -13 74 57 -135 48 -320 73 -42 -36 60 20 -27 -7 65 -34 -27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWWGATGACGTVDNH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6091 E= 3.5e-394 0.343129 0.113118 0.297816 0.245937 0.411427 0.112625 0.177475 0.298473 0.276966 0.155639 0.145461 0.421934 0.180923 0.091446 0.592021 0.135610 0.556395 0.217042 0.220653 0.005910 0.001149 0.000821 0.000000 0.998030 0.000164 0.000000 0.906748 0.093088 0.999179 0.000000 0.000000 0.000821 0.000328 0.846987 0.000328 0.152356 0.051716 0.002791 0.944672 0.000821 0.118207 0.043014 0.015268 0.823510 0.285996 0.312921 0.278608 0.122476 0.435068 0.020358 0.311279 0.233295 0.242817 0.283533 0.215071 0.258578 0.297652 0.294697 0.147923 0.259727 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWWGATGACGTVDNH MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][AT][TA]G[AGC]TGACGT[CAG][AGT][CTAG][ACT] -------------------------------------------------------------------------------- Time 70.46 secs. ******************************************************************************** ******************************************************************************** MOTIF YTTYTTCTYYTTCTYYYTYTY MEME-2 width = 21 sites = 1565 llr = 15629 E-value = 2.0e-064 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTTYTTCTYYTTCTYYYTYTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 12::::1:::11:1:::112: pos.-specific C 422431614521614432514 probability G 1:2:1::1::1:11::2:111 matrix T 366569376568376557365 bits 2.4 2.2 1.9 1.7 Relative 1.4 Entropy 1.2 * (14.4 bits) 1.0 ** ** * ** 0.7 ******* ** ** * * 0.5 ************ ***** * 0.2 ********************* 0.0 --------------------- Multilevel CTTTTTCTTTTTCTTTTTCTT consensus TACCC T CCC T CCCCT C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTYTTCTYYTTCTYYYTYTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1199735 bayes= 11.8747 E= 2.0e-064 -115 110 -60 10 -39 0 -1726 87 -300 24 -18 88 -287 120 -258 66 -1726 55 -114 104 -1726 -34 -1726 145 -238 179 -819 -11 -893 -63 -53 126 -1726 99 -1726 101 -1726 127 -719 81 -235 30 -68 92 -243 -41 -193 127 -423 174 -117 -20 -120 -112 -59 106 -1726 102 -719 99 -893 126 -1726 81 -1726 73 3 67 -249 35 -1726 117 -196 151 -174 7 -92 -61 -38 86 -1726 94 -46 69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTYTTCTYYTTCTYYYTYTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1565 E= 2.0e-064 0.141214 0.400639 0.123323 0.334824 0.238978 0.187859 0.000000 0.573163 0.038978 0.221725 0.164856 0.574441 0.042812 0.431310 0.031310 0.494569 0.000000 0.274121 0.084984 0.640895 0.000000 0.147604 0.000000 0.852396 0.060064 0.649840 0.000639 0.289457 0.000639 0.121406 0.129712 0.748243 0.000000 0.371885 0.000000 0.628115 0.000000 0.451118 0.001278 0.547604 0.061342 0.231310 0.116933 0.590415 0.058147 0.141214 0.049201 0.751438 0.016613 0.628115 0.083067 0.272204 0.136102 0.086262 0.124601 0.653035 0.000000 0.379553 0.001278 0.619169 0.000639 0.449840 0.000000 0.549521 0.000000 0.311182 0.191054 0.497764 0.055591 0.238978 0.000000 0.705431 0.080511 0.534824 0.056230 0.328435 0.164856 0.122684 0.144409 0.568051 0.000000 0.359744 0.136102 0.504153 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTTYTTCTYYTTCTYYYTYTY MEME-2 regular expression -------------------------------------------------------------------------------- [CT][TA][TC][TC][TC]T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC][TC][CT]T[TC] -------------------------------------------------------------------------------- Time 130.30 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************