******************************************************************************** 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/AT5G09410_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/AT5G09410_peak_sequences.fasta -dna -oc out/AT5G09410 -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= 5999 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= 1306262 N= 5999 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.302 C 0.198 G 0.198 T 0.302 Background letter frequencies (from file dataset with add-one prior applied): A 0.304 C 0.196 G 0.196 T 0.304 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DWAAVCGCGTK MEME-1 width = 11 sites = 5972 llr = 47505 E-value = 5.9e-344 ******************************************************************************** -------------------------------------------------------------------------------- Motif DWAAVCGCGTK MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34554:::::2 pos.-specific C 112:4a:8::2 probability G 32122:a:a:3 matrix T 2322:::2:a3 bits 2.4 ** * 2.1 ** * 1.9 ** * 1.6 ** ** Relative 1.4 ***** Entropy 1.2 ***** (11.5 bits) 0.9 ***** 0.7 ***** 0.5 ****** 0.2 ********* 0.0 ----------- Multilevel AAAACCGCGTT consensus GTTGA G sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWAAVCGCGTK MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1246272 bayes= 9.79718 E= 5.9e-344 6 -57 64 -30 51 -51 -24 -22 83 -31 -137 -44 82 -252 26 -66 28 95 33 -543 -1919 235 -1919 -1919 -1919 -1919 235 -1919 -683 203 -1919 -64 -1919 -1919 235 -1919 -1919 -1919 -611 171 -90 -35 80 17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWAAVCGCGTK MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5972 E= 5.9e-344 0.316142 0.131949 0.304588 0.247321 0.434193 0.138145 0.166443 0.261219 0.542029 0.157904 0.075854 0.224213 0.538346 0.034159 0.234595 0.192900 0.369390 0.377763 0.245814 0.007033 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.002679 0.802244 0.000000 0.195077 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.002847 0.997153 0.163262 0.154052 0.340589 0.342096 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWAAVCGCGTK MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][AT][AT][AG][CAG]CGCGT[TG] -------------------------------------------------------------------------------- Time 75.25 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARAARAARAARAARARRAA MEME-2 width = 21 sites = 1281 llr = 14208 E-value = 1.3e-086 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARAARAARAARAARARRAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 46648657a485578485567 pos.-specific C 1:21111:::11::1:1:111 probability G 43251343:613431513432 matrix T 111::1:::::1::1::1::: bits 2.4 2.1 1.9 1.6 * Relative 1.4 * Entropy 1.2 * (16.0 bits) 0.9 * **** ** ** 0.7 * ** ***** ***** ** 0.5 * ******** ********* 0.2 ********************* 0.0 --------------------- Multilevel AAAGAAAAAGAAAAAGAAAAA consensus GG A GGG A GGG A GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARARRAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1186282 bayes= 12.141 E= 1.3e-086 49 -174 96 -120 107 -797 66 -256 92 -11 -30 -184 28 -114 147 -1697 145 -184 -75 -1697 90 -72 36 -226 74 -167 113 -1697 110 -269 70 -1697 172 -1697 -1697 -1697 25 -302 165 -1697 148 -150 -193 -325 80 -59 38 -186 79 -276 118 -1697 118 -1697 57 -408 138 -153 -131 -228 52 -255 144 -1697 147 -130 -137 -1697 85 -1697 63 -104 63 -63 90 -305 109 -120 45 -1697 120 -75 -10 -860 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARARRAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1281 E= 1.3e-086 0.427010 0.058548 0.381733 0.132709 0.638564 0.000781 0.309133 0.051522 0.573770 0.181889 0.159251 0.085090 0.368462 0.088993 0.542545 0.000000 0.829040 0.054645 0.116315 0.000000 0.566745 0.118657 0.251366 0.063232 0.508977 0.061671 0.429352 0.000000 0.651835 0.030445 0.317721 0.000000 1.000000 0.000000 0.000000 0.000000 0.361436 0.024200 0.614364 0.000000 0.846995 0.069477 0.051522 0.032006 0.530055 0.130367 0.256050 0.083528 0.526932 0.028884 0.444184 0.000000 0.690867 0.000000 0.291179 0.017955 0.790788 0.067916 0.078845 0.062451 0.434817 0.033568 0.531616 0.000000 0.844653 0.079625 0.075722 0.000000 0.548790 0.000000 0.303669 0.147541 0.469945 0.126464 0.366901 0.036690 0.647151 0.085090 0.267760 0.000000 0.700234 0.116315 0.182670 0.000781 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARAARAARARRAA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG]A[GA]A[AG][AG][AG]A[GA]A[AG][AG][AG]A[GA]A[AG][AG][AG]A -------------------------------------------------------------------------------- Time 137.14 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************