******************************************************************************** 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/AT3G17730_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/AT3G17730_peak_sequences.fasta -dna -oc out/AT3G17730 -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= 4700 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= 1110119 N= 4700 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 TTNCTTSHNNHWCAMGYHWYY MEME-1 width = 21 sites = 4686 llr = 41735 E-value = 7.6e-460 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTNCTTSHNNHWCAMGYHWYY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 123:::122223:a5:13622 pos.-specific C :12a::3223326:4:32:44 probability G :13:2:5122211::81::12 matrix T 863:8a1443442::144433 bits 2.4 2.2 * 1.9 * 1.7 * * Relative 1.4 * * * * Entropy 1.2 * * * * (12.8 bits) 1.0 * *** *** 0.7 * *** **** 0.5 * **** **** * 0.2 ** **** ********* 0.0 --------------------- Multilevel TTTCTTGTTTTTCAAGTTACC consensus G CAACCAT C CATTT sequence A CC C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTSHNNHWCAMGYHWYY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1016119 bayes= 9.65869 E= 7.6e-460 -141 -259 -373 143 -83 -173 -48 102 -31 -10 57 -9 -519 238 -633 -581 -626 -389 -12 138 -575 -327 -533 164 -178 48 145 -128 -40 13 -42 42 -37 10 5 22 -76 60 5 10 -64 55 -14 18 4 -13 -55 29 -264 167 -76 -39 163 -389 -366 -526 79 124 -349 -1884 -530 -647 215 -106 -155 85 -54 45 12 30 -379 42 95 -308 -332 21 -82 101 -93 15 -91 117 -33 -27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTSHNNHWCAMGYHWYY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4686 E= 7.6e-460 0.117157 0.031370 0.014298 0.837175 0.174563 0.057192 0.136150 0.632096 0.250107 0.176697 0.281050 0.292147 0.008536 0.983568 0.002347 0.005548 0.004055 0.012804 0.174349 0.808792 0.005762 0.019633 0.004695 0.969910 0.090269 0.263338 0.518779 0.127614 0.234955 0.207853 0.141912 0.415280 0.239650 0.202732 0.195689 0.361929 0.182885 0.287665 0.196543 0.332907 0.199104 0.276569 0.172002 0.352326 0.318609 0.172855 0.129108 0.379428 0.049936 0.601366 0.111396 0.237303 0.964149 0.012804 0.014938 0.008109 0.537132 0.446009 0.016859 0.000000 0.007896 0.002134 0.840802 0.149168 0.106274 0.340376 0.130388 0.422962 0.338668 0.233035 0.013658 0.414639 0.599445 0.022407 0.018993 0.359155 0.175416 0.380922 0.099659 0.344003 0.165600 0.425096 0.150875 0.258429 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTSHNNHWCAMGYHWYY MEME-1 regular expression -------------------------------------------------------------------------------- TT[TGA]CTT[GC][TAC][TAC][TC][TC][TA][CT]A[AC]G[TC][TAC][AT][CT][CT] -------------------------------------------------------------------------------- Time 75.10 secs. ******************************************************************************** ******************************************************************************** MOTIF RAGARRAARAARAARARRARR MEME-2 width = 21 sites = 1581 llr = 15088 E-value = 2.9e-062 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAGARRAARAARAARARRARR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 463954693865664855755 pos.-specific C 111:111:::::11::11:12 probability G 3161343:6134226135233 matrix T 12::::::::1:11:11:111 bits 2.4 2.2 1.9 1.7 Relative 1.4 Entropy 1.2 * ** (13.8 bits) 1.0 ** *** * * 0.7 ** **** * ** ** 0.5 ********** ***** 0.2 ********************* 0.0 --------------------- Multilevel AAGAAAAAGAAAAAGAAAAAA consensus G A GGG A GG A GG GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGARRAARAARAARARRARR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1016119 bayes= 11.5922 E= 2.9e-062 45 -40 79 -157 97 -61 -123 -73 -12 -151 177 -1727 148 -1727 -65 -469 79 -69 65 -265 53 -77 113 -345 95 -84 64 -1727 152 -383 -194 -277 15 -1727 175 -394 143 -1727 -41 -419 102 -290 55 -216 81 -314 120 -1727 94 -46 6 -216 97 -41 -25 -183 36 -1727 159 -321 132 -232 -121 -154 74 -120 79 -211 65 -187 128 -1727 126 -250 -20 -239 75 -169 68 -142 58 -30 74 -223 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGARRAARAARAARARRARR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1581 E= 2.9e-062 0.425047 0.143580 0.326376 0.104997 0.607211 0.123972 0.080961 0.187856 0.286528 0.066414 0.647059 0.000000 0.867173 0.000000 0.120810 0.012018 0.537002 0.117015 0.296648 0.049336 0.447818 0.110689 0.413030 0.028463 0.598988 0.105629 0.295383 0.000000 0.891841 0.013283 0.049336 0.045541 0.344086 0.000000 0.635674 0.020240 0.839975 0.000000 0.142948 0.017078 0.628716 0.025300 0.276407 0.069576 0.544592 0.021505 0.433903 0.000000 0.595193 0.137887 0.197343 0.069576 0.610373 0.142948 0.159393 0.087287 0.398482 0.000000 0.567995 0.033523 0.773561 0.037951 0.081594 0.106894 0.518659 0.082226 0.327008 0.072106 0.488299 0.051866 0.459836 0.000000 0.742568 0.033523 0.164453 0.059456 0.522454 0.058824 0.302973 0.115750 0.464263 0.153700 0.315623 0.066414 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAGARRAARAARAARARRARR MEME-2 regular expression -------------------------------------------------------------------------------- [AG]A[GA]A[AG][AG][AG]A[GA]A[AG][AG]AA[GA]A[AG][AG]A[AG][AG] -------------------------------------------------------------------------------- Time 141.75 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************