******************************************************************************** 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/AT1G36060_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/AT1G36060_peak_sequences.fasta -dna -oc out/AT1G36060 -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= 3402 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= 630429 N= 3402 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.277 C 0.223 G 0.223 T 0.277 Background letter frequencies (from file dataset with add-one prior applied): A 0.28 C 0.22 G 0.22 T 0.28 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YCACCGACMWHWHH MEME-1 width = 14 sites = 3304 llr = 28226 E-value = 1.4e-597 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCACCGACMWHWHH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 117:::6:454332 pos.-specific C 58:aa:2a422123 probability G 113::a::111211 matrix T 3:::::2:134443 bits 2.2 *** * 2.0 *** * 1.7 *** * 1.5 *** * Relative 1.3 *** * Entropy 1.1 ***** * (12.3 bits) 0.9 ***** * 0.7 ***** * 0.4 ******* 0.2 *********** 0.0 -------------- Multilevel CCACCGACAATTTC consensus T G T CTAAAT sequence C CA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACCGACMWHWHH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 14 n= 586203 bayes= 9.09447 E= 1.4e-597 -130 111 -82 4 -112 181 -186 -278 130 -1833 47 -605 -753 218 -1833 -1833 -1833 218 -1833 -1833 -685 -1833 218 -1833 107 -37 -291 -40 -1833 218 -850 -1833 57 82 -103 -168 82 -34 -175 -7 35 -9 -200 45 27 -81 -43 41 -3 15 -96 40 -20 62 -109 17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACCGACMWHWHH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 14 nsites= 3304 E= 1.4e-597 0.113801 0.473971 0.124697 0.287530 0.128935 0.769370 0.060835 0.040860 0.690981 0.000000 0.304782 0.004237 0.001513 0.998487 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.002421 0.000000 0.997579 0.000000 0.587772 0.170702 0.029358 0.212167 0.000000 0.999395 0.000605 0.000000 0.415557 0.389225 0.107748 0.087470 0.494249 0.174334 0.065375 0.266041 0.356840 0.207022 0.055085 0.381053 0.338378 0.125303 0.163741 0.372579 0.274213 0.244552 0.112893 0.368341 0.243947 0.337772 0.103208 0.315073 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCACCGACMWHWHH MEME-1 regular expression -------------------------------------------------------------------------------- [CT]C[AG]CCG[AT]C[AC][AT][TAC][TA][TAC][CTA] -------------------------------------------------------------------------------- Time 128.39 secs. ******************************************************************************** ******************************************************************************** MOTIF WYCNYCDYCKYCTCCKYCKYC MEME-2 width = 21 sites = 1117 llr = 11343 E-value = 4.1e-119 ******************************************************************************** -------------------------------------------------------------------------------- Motif WYCNYCDYCKYCTCCKYCKYC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 3112:13112::1::2::1:: pos.-specific C 156248157149:78169:67 probability G 11121:31:2::2::3::4:: matrix T 532341432451731441433 bits 2.2 2.0 1.7 * 1.5 * * Relative 1.3 * * * * Entropy 1.1 * * * * * * (14.7 bits) 0.9 * * ** ** ** * 0.7 * * ***** ** ** 0.4 * ** * ***** ***** 0.2 *** ** ************** 0.0 --------------------- Multilevel TCCTTCTCCTTCTCCTCCTCC consensus ATTGC GTTGC GT GT GTT sequence C A A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYCNYCDYCKYCTCCKYCKYC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 562389 bayes= 11.1406 E= 4.1e-119 -5 -60 -84 72 -153 115 -58 -6 -91 138 -192 -33 -44 -3 14 26 -283 95 -130 67 -229 189 -1677 -115 -15 -107 34 38 -123 119 -98 -6 -246 168 -594 -22 -37 -116 12 67 -1677 101 -355 94 -1677 202 -362 -163 -136 -1677 2 125 -629 158 -239 8 -316 191 -448 -112 -57 -177 66 51 -329 140 -348 41 -1677 206 -1677 -181 -92 -1677 94 62 -383 141 -219 31 -497 164 -308 1 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYCNYCDYCKYCTCCKYCKYC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1117 E= 4.1e-119 0.271262 0.145031 0.122650 0.461056 0.096688 0.487914 0.147717 0.267681 0.148612 0.571173 0.058192 0.222023 0.205909 0.215756 0.242614 0.335721 0.039391 0.424351 0.089526 0.446732 0.057296 0.816473 0.000000 0.126231 0.251567 0.104745 0.278424 0.365264 0.119069 0.501343 0.111907 0.267681 0.051030 0.705461 0.003581 0.239928 0.216652 0.098478 0.239033 0.445837 0.000000 0.444047 0.018800 0.537153 0.000000 0.891674 0.017905 0.090421 0.109221 0.000000 0.222919 0.667860 0.003581 0.658013 0.042077 0.296329 0.031334 0.829902 0.009848 0.128917 0.188899 0.064458 0.348254 0.398389 0.028648 0.580125 0.019696 0.371531 0.000000 0.920322 0.000000 0.079678 0.147717 0.000000 0.423456 0.428827 0.019696 0.584602 0.048344 0.347359 0.008953 0.683975 0.025962 0.281110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYCNYCDYCKYCTCCKYCKYC MEME-2 regular expression -------------------------------------------------------------------------------- [TA][CT][CT][TGCA][TC]C[TGA][CT][CT][TGA][TC]C[TG][CT]C[TG][CT]C[TG][CT][CT] -------------------------------------------------------------------------------- Time 239.71 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************