******************************************************************************** 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/AT2G46590_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/AT2G46590_peak_sequences.fasta -dna -oc out/AT2G46590 -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= 7793 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= 2200329 N= 7793 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.361 C 0.139 G 0.139 T 0.361 Background letter frequencies (from file dataset with add-one prior applied): A 0.361 C 0.139 G 0.139 T 0.361 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HTYTTTTTYTYTTTTTTTTTT MEME-1 width = 21 sites = 4425 llr = 43299 E-value = 2.7e-187 ******************************************************************************** -------------------------------------------------------------------------------- Motif HTYTTTTTYTYTTTTTTTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 21:1:1:::1::1:::1:::: pos.-specific C 413133314:43213232213 probability G 111:::1::1:::111:1112 matrix T 376877696867786768686 bits 2.8 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 (14.1 bits) 1.1 * 0.9 * * *** ** * * * 0.6 ******************* 0.3 ********************* 0.0 --------------------- Multilevel CTTTTTTTTTTTTTTTTTTTT consensus T C CCC C CC CCC C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTTTTTYTYTTTTTTTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2044469 bayes= 11.132 E= 2.7e-187 -88 134 -6 -18 -158 -51 -54 93 -806 131 -92 69 -182 -43 -271 110 -536 105 -1876 96 -252 100 -1876 87 -1876 98 -65 82 -363 -98 -1876 132 -491 149 -257 67 -139 -926 -121 115 -387 134 -279 74 -393 99 -1876 95 -224 30 -157 97 -410 -35 -134 117 -391 90 -46 77 -447 54 -130 101 -184 89 -1876 83 -1876 32 -95 106 -319 47 -8 82 -339 -79 -110 118 -864 86 34 66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTTTTTYTYTTTTTTTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4425 E= 2.7e-187 0.196158 0.352090 0.132655 0.319096 0.120678 0.097401 0.095141 0.686780 0.001356 0.343955 0.073220 0.581469 0.102147 0.103277 0.021243 0.773333 0.008814 0.287232 0.000000 0.703955 0.063051 0.277740 0.000000 0.659209 0.000000 0.274350 0.088136 0.637514 0.029153 0.070282 0.000000 0.900565 0.011977 0.389153 0.023277 0.575593 0.137853 0.000226 0.059887 0.802034 0.024633 0.350282 0.020113 0.604972 0.023729 0.275932 0.000000 0.700339 0.076384 0.171073 0.046780 0.705763 0.021017 0.108701 0.054915 0.815367 0.023955 0.259209 0.101017 0.615819 0.016271 0.201356 0.056497 0.725876 0.101017 0.256723 0.000000 0.642260 0.000000 0.172881 0.071864 0.755254 0.039548 0.192768 0.131073 0.636610 0.034350 0.080226 0.064859 0.820565 0.000904 0.251525 0.176045 0.571525 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTTTTTYTYTTTTTTTTTT MEME-1 regular expression -------------------------------------------------------------------------------- [CT]T[TC]T[TC][TC][TC]T[TC]T[TC][TC]TT[TC][TC][TC]TTT[TC] -------------------------------------------------------------------------------- Time 73.77 secs. ******************************************************************************** ******************************************************************************** MOTIF MCTTTTTB MEME-2 width = 8 sites = 7740 llr = 53312 E-value = 1.1e-100 ******************************************************************************** -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5::::::1 pos.-specific C 3a::::13 probability G 1::::::2 matrix T ::aaaa84 bits 2.8 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.9 bits) 1.1 ***** 0.9 ****** 0.6 ******* 0.3 ******** 0.0 -------- Multilevel ACTTTTTT consensus C C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 2145778 bayes= 10.2564 E= 1.1e-100 52 118 -17 -311 -1956 285 -1956 -1956 -1956 -648 -1956 147 -1956 -1956 -1956 147 -1956 -1956 -1956 147 -329 -1956 -1956 141 -351 -31 -171 117 -128 104 60 -2 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7740 E= 1.1e-100 0.519509 0.314987 0.123514 0.041990 0.000000 1.000000 0.000000 0.000000 0.000000 0.001550 0.000000 0.998450 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.036822 0.000000 0.000000 0.963178 0.031654 0.112145 0.042377 0.813824 0.148579 0.285788 0.209948 0.355685 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MCTTTTTB MEME-2 regular expression -------------------------------------------------------------------------------- [AC]CTTTTT[TCG] -------------------------------------------------------------------------------- Time 141.99 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************