******************************************************************************** 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/AT1G25340_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/AT1G25340_peak_sequences.fasta -dna -oc out/AT1G25340 -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= 3880 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= 696439 N= 3880 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.331 C 0.169 G 0.169 T 0.331 Background letter frequencies (from file dataset with add-one prior applied): A 0.333 C 0.168 G 0.168 T 0.333 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAARTTAGGYADA MEME-1 width = 13 sites = 3874 llr = 31951 E-value = 7.3e-553 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAARTTAGGYADA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5573::8:::535 pos.-specific C 11:::::::5221 probability G 22161::aa:232 matrix T 332:9a1::5222 bits 2.6 ** 2.3 ** 2.1 ** 1.8 ** Relative 1.5 * ** Entropy 1.3 ** ** (11.9 bits) 1.0 *** *** 0.8 ******* 0.5 ******** 0.3 ********* * 0.0 ------------- Multilevel AAAGTTAGGCAAA consensus TT A T GG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAARTTAGGYADA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 649879 bayes= 9.05207 E= 7.3e-553 44 -56 -9 -26 68 -163 -10 -36 100 -464 -33 -76 -1 -1856 193 -332 -1856 -1856 -150 150 -1856 -634 -1856 159 134 -298 -367 -140 -1856 -1856 258 -1856 -752 -1856 257 -733 -663 160 -336 51 52 14 13 -109 7 -10 64 -50 54 -69 48 -90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAARTTAGGYADA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 3874 E= 7.3e-553 0.450697 0.113578 0.157718 0.278007 0.530976 0.053949 0.156427 0.258647 0.663913 0.006711 0.133454 0.195922 0.329892 0.000000 0.636809 0.033299 0.000000 0.000000 0.059370 0.940630 0.000000 0.002065 0.000000 0.997935 0.839701 0.021167 0.013165 0.125968 0.000000 0.000000 1.000000 0.000000 0.001807 0.000000 0.996128 0.002065 0.003356 0.508518 0.016262 0.471864 0.475478 0.184564 0.183789 0.156169 0.348735 0.156169 0.260712 0.234383 0.483738 0.103769 0.234383 0.178110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAARTTAGGYADA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT]A[GA]TTAGG[CT]A[AGT][AG] -------------------------------------------------------------------------------- Time 126.26 secs. ******************************************************************************** ******************************************************************************** MOTIF TBGGTTYGGTTYGGT MEME-2 width = 15 sites = 108 llr = 1497 E-value = 6.0e-008 ******************************************************************************** -------------------------------------------------------------------------------- Motif TBGGTTYGGTTYGGT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::1:::::1::::1 pos.-specific C 34::::5:::151:: probability G :3a7:::8a3::683 matrix T 73:2aa52:695326 bits 2.6 * 2.3 * * 2.1 * * 1.8 * ** * Relative 1.5 * ** ** * Entropy 1.3 * ** ** * * (20.0 bits) 1.0 * ******* **** 0.8 ********* **** 0.5 *************** 0.3 *************** 0.0 --------------- Multilevel TCGGTTCGGTTCGGT consensus CG T T G TT G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBGGTTYGGTTYGGT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 642119 bayes= 14.6602 E= 6.0e-008 -1340 63 -1340 116 -1340 125 99 -31 -317 -1340 252 -1340 -171 -1340 201 -58 -1340 -1340 -318 156 -1340 -1340 -417 158 -1340 158 -1340 59 -1340 -1340 233 -108 -1340 -1340 258 -1340 -200 -1340 78 92 -1340 -137 -1340 149 -1340 166 -1340 51 -1340 -37 189 -41 -1340 -1340 228 -84 -200 -1340 82 90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBGGTTYGGTTYGGT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 108 E= 6.0e-008 0.000000 0.259259 0.000000 0.740741 0.000000 0.398148 0.333333 0.268519 0.037037 0.000000 0.962963 0.000000 0.101852 0.000000 0.675926 0.222222 0.000000 0.000000 0.018519 0.981481 0.000000 0.000000 0.009259 0.990741 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.842593 0.157407 0.000000 0.000000 1.000000 0.000000 0.083333 0.000000 0.287037 0.629630 0.000000 0.064815 0.000000 0.935185 0.000000 0.527778 0.000000 0.472222 0.000000 0.129630 0.620370 0.250000 0.000000 0.000000 0.814815 0.185185 0.083333 0.000000 0.296296 0.620370 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TBGGTTYGGTTYGGT MEME-2 regular expression -------------------------------------------------------------------------------- [TC][CGT]G[GT]TT[CT]GG[TG]T[CT][GT]G[TG] -------------------------------------------------------------------------------- Time 235.70 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************