******************************************************************************** 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/AT1G22070_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/AT1G22070_peak_sequences.fasta -dna -oc out/AT1G22070 -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= 5640 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= 1192892 N= 5640 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 0.311 C 0.189 G 0.189 T 0.311 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DWHDNYBACGTCA MEME-1 width = 13 sites = 5611 llr = 42996 E-value = 6.2e-435 ******************************************************************************** -------------------------------------------------------------------------------- Motif DWHDNYBACGTCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 43333219:1:1a pos.-specific C 2221233:a::9: probability G 22233:31:9::: matrix T 33432531::a:: bits 2.4 * 2.2 * * 1.9 * * 1.7 ***** Relative 1.4 ***** Entropy 1.2 ***** (11.1 bits) 1.0 ****** 0.7 ****** 0.5 ****** 0.2 ******** 0.0 ------------- Multilevel AATGATGACGTCA consensus TTATGCT sequence G CATAC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWHDNYBACGTCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 1125212 bayes= 9.72611 E= 6.2e-435 18 -26 25 -23 15 -20 -23 8 -17 21 -32 18 -29 -61 85 -14 0 10 55 -57 -57 65 -221 54 -168 52 78 -1 145 -476 -181 -184 -1910 239 -624 -516 -125 -1910 221 -1910 -1910 -688 -1910 168 -247 232 -1910 -1910 168 -1910 -1910 -1910 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWHDNYBACGTCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 5611 E= 6.2e-435 0.353769 0.157369 0.223668 0.265193 0.345393 0.163785 0.161112 0.329709 0.277312 0.218321 0.151488 0.352878 0.254500 0.123329 0.339690 0.282481 0.311709 0.202638 0.275530 0.210123 0.209945 0.296026 0.040634 0.453395 0.097487 0.269471 0.323294 0.309749 0.852255 0.006951 0.053823 0.086972 0.000000 0.988772 0.002495 0.008733 0.130814 0.000000 0.869186 0.000000 0.000000 0.001604 0.000000 0.998396 0.056140 0.943860 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DWHDNYBACGTCA MEME-1 regular expression -------------------------------------------------------------------------------- [ATG][AT][TAC][GTA][AGTC][TCA][GTC]ACGTCA -------------------------------------------------------------------------------- Time 124.41 secs. ******************************************************************************** ******************************************************************************** MOTIF RRRRARARRRAGAVRRAGRARRAGAARR MEME-2 width = 28 sites = 831 llr = 9705 E-value = 9.6e-056 ******************************************************************************** -------------------------------------------------------------------------------- Motif RRRRARARRRAGAVRRAGRARRAGAARR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5445636564737444936664837635 pos.-specific C 121:1:12::1::21::::1::1::111 probability G 3244163335:73345:73245172263 matrix T :111111:1121111:1::1::1:1211 bits 2.4 2.2 1.9 1.7 Relative 1.4 Entropy 1.2 * * (16.8 bits) 1.0 * *** ** * 0.7 * * ** **** ***** 0.5 * * ******** ***** ***** * 0.2 * ************************** 0.0 ---------------------------- Multilevel AAGAAGAAAGAGAAAGAGAAAGAGAAGA consensus GGAG AGGGATAGGGA AGGGA AG AG sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRRRARARRRAGAVRRAGRARRAGAARR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 1040612 bayes= 12.5049 E= 9.6e-056 75 -66 75 -302 44 13 30 -116 23 -75 109 -134 67 -1634 122 -223 95 -56 -48 -118 9 -1634 163 -191 92 -162 44 -173 58 -30 82 -273 90 -238 74 -218 48 -212 131 -249 112 -108 -1634 -42 -32 -320 180 -213 111 -1634 46 -216 32 26 57 -156 50 -148 117 -218 51 -277 149 -1634 150 -1634 -1634 -136 -19 -448 184 -289 94 -201 84 -402 82 -60 20 -152 89 -304 108 -1634 52 -259 147 -1634 131 -65 -190 -246 -7 -412 188 -1634 117 -1634 29 -218 84 -88 -33 -70 -9 -156 156 -181 60 -123 69 -112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRRRARARRRAGAVRRAGRARRAGAARR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 831 E= 9.6e-056 0.524669 0.119134 0.317690 0.038508 0.421179 0.206980 0.232250 0.139591 0.364621 0.111913 0.400722 0.122744 0.495788 0.000000 0.438026 0.066185 0.600481 0.127557 0.134777 0.137184 0.332130 0.000000 0.584838 0.083032 0.589651 0.061372 0.255114 0.093863 0.466907 0.152828 0.333333 0.046931 0.580024 0.036101 0.315283 0.068592 0.434416 0.043321 0.466907 0.055355 0.678700 0.089049 0.000000 0.232250 0.250301 0.020457 0.658243 0.070999 0.671480 0.000000 0.258724 0.069795 0.388688 0.226233 0.279182 0.105897 0.439230 0.067389 0.424789 0.068592 0.442840 0.027677 0.529483 0.000000 0.878460 0.000000 0.000000 0.121540 0.273165 0.008424 0.676294 0.042118 0.596871 0.046931 0.336943 0.019254 0.551143 0.123947 0.216606 0.108303 0.577617 0.022864 0.399519 0.000000 0.445247 0.031288 0.523466 0.000000 0.772563 0.120337 0.050542 0.056558 0.296029 0.010830 0.693141 0.000000 0.700361 0.000000 0.231047 0.068592 0.555957 0.102286 0.150421 0.191336 0.292419 0.063779 0.554753 0.089049 0.472924 0.080626 0.303249 0.143201 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRRRARARRRAGAVRRAGRARRAGAARR MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AGC][GA][AG]A[GA][AG][AG][AG][GA][AT][GA][AG][AGC][AG][GA]A[GA][AG][AG][AG][GA]A[GA][AG]A[GA][AG] -------------------------------------------------------------------------------- Time 234.01 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************