******************************************************************************** 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/AT2G01930_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/AT2G01930_peak_sequences.fasta -dna -oc out/AT2G01930 -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= 2112 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= 291555 N= 2112 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.31 C 0.19 G 0.19 T 0.31 Background letter frequencies (from file dataset with add-one prior applied): A 0.31 C 0.19 G 0.19 T 0.31 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTYTCTCTCTCTCTCTYTYTY MEME-1 width = 21 sites = 1936 llr = 29708 E-value = 3.2e-2726 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTYTCTCTCTCTCTCTYTYTY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 11::::::::::::1:11111 pos.-specific C 61617:8:9:9:817262525 probability G 1:::::::::::::::::::1 matrix T 3739392a1a1a282736474 bits 2.4 2.2 1.9 * 1.7 * *** Relative 1.4 ******** Entropy 1.2 ******** (22.1 bits) 1.0 ************ 0.7 *************** 0.5 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CTCTCTCTCTCTCTCTCTCTC consensus T T T T TCTCT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTCTCTCTCTCTCTYTYTY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 249315 bayes= 9.23592 E= 3.2e-2726 -139 157 -173 -26 -144 -40 -482 124 -312 167 -208 2 -274 -116 -339 146 -287 182 -382 -18 -442 -239 -1756 161 -691 215 -1756 -102 -459 -413 -520 165 -402 225 -366 -225 -1756 -852 -652 168 -553 231 -752 -260 -642 -297 -1756 165 -442 211 -452 -95 -300 -61 -1756 143 -263 187 -435 -31 -275 0 -225 122 -180 154 -200 1 -139 21 -282 103 -123 138 -313 19 -239 34 -215 108 -149 134 -178 20 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTCTCTCTCTCTCTYTYTY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1936 E= 3.2e-2726 0.118802 0.564050 0.057335 0.259814 0.114669 0.143595 0.006715 0.735021 0.035640 0.603822 0.044938 0.315599 0.046488 0.084711 0.018079 0.850723 0.042355 0.670455 0.013430 0.273760 0.014463 0.036157 0.000000 0.949380 0.002583 0.844525 0.000000 0.152893 0.012913 0.010847 0.005165 0.971074 0.019112 0.900826 0.014979 0.065083 0.000000 0.000517 0.002066 0.997417 0.006715 0.941116 0.001033 0.051136 0.003616 0.024277 0.000000 0.972107 0.014463 0.816116 0.008264 0.161157 0.038740 0.124483 0.000000 0.836777 0.050103 0.691116 0.009298 0.249483 0.045971 0.189050 0.039773 0.725207 0.089360 0.550103 0.047521 0.313017 0.118802 0.220041 0.026860 0.634298 0.132231 0.493285 0.021694 0.352789 0.059401 0.240186 0.042872 0.657541 0.110537 0.478822 0.055269 0.355372 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTYTCTCTCTCTCTCTYTYTY MEME-1 regular expression -------------------------------------------------------------------------------- [CT]T[CT]T[CT]TCTCTCTCT[CT]T[CT][TC][CT][TC][CT] -------------------------------------------------------------------------------- Time 125.68 secs. ******************************************************************************** ******************************************************************************** MOTIF RARAGAGARAGARRRAGARRR MEME-2 width = 21 sites = 1153 llr = 12459 E-value = 5.5e-636 ******************************************************************************** -------------------------------------------------------------------------------- Motif RARAGAGARAGARRRAGARRR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 373829284928465638564 pos.-specific C 1:::::::::::1::1::::1 probability G 52627:626171434262444 matrix T 11::::1:::1:1111::111 bits 2.4 2.2 1.9 1.7 Relative 1.4 Entropy 1.2 ** * (15.6 bits) 1.0 ** *** * 0.7 *********** ** * 0.5 ************ ******* 0.2 ********************* 0.0 --------------------- Multilevel GAGAGAGAGAGAGAAAGAAAA consensus AGA A A A A AGGGA GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAGAGARAGARRRAGARRR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 249315 bayes= 10.0571 E= 5.5e-636 8 -120 141 -187 117 -1682 37 -242 14 -235 159 -268 130 -319 -17 -281 -55 -219 194 -431 155 -297 -225 -362 -47 -202 177 -194 128 -228 -2 -384 19 -205 162 -396 148 -545 -105 -313 -55 -545 193 -240 144 -282 -100 -299 31 -133 112 -128 86 -331 77 -174 55 -202 118 -222 102 -173 19 -168 -3 -213 173 -368 130 -260 -19 -302 57 -431 115 -152 89 -1682 96 -253 36 -111 106 -140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAGAGARAGARRRAGARRR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1153 E= 5.5e-636 0.326973 0.082394 0.505637 0.084996 0.697311 0.000000 0.244579 0.058109 0.342585 0.037294 0.571552 0.048569 0.766696 0.020815 0.168257 0.044232 0.212489 0.041631 0.730269 0.015611 0.910668 0.024284 0.039896 0.025152 0.223764 0.046834 0.648742 0.080659 0.751951 0.039029 0.187337 0.021683 0.352992 0.045967 0.581093 0.019948 0.868170 0.004337 0.091934 0.035559 0.212489 0.004337 0.724198 0.058977 0.839549 0.026886 0.094536 0.039029 0.384215 0.075455 0.412836 0.127493 0.564614 0.019081 0.323504 0.092801 0.455334 0.046834 0.431049 0.066782 0.629662 0.057242 0.215958 0.097138 0.303556 0.043365 0.628794 0.024284 0.764094 0.031223 0.166522 0.038161 0.461405 0.009540 0.420642 0.108413 0.576756 0.000000 0.369471 0.053773 0.398092 0.087598 0.396357 0.117953 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAGAGARAGARRRAGARRR MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG][GA]A[GA]A[GA]A[GA]A[GA]A[GA][AG][AG][AG][GA]A[AG][AG][AG] -------------------------------------------------------------------------------- Time 225.54 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************