******************************************************************************** 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/AT5G66940_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/AT5G66940_peak_sequences.fasta -dna -oc out/AT5G66940 -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= 7934 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= 1917519 N= 7934 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.36 C 0.14 G 0.14 T 0.36 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 AAAAAGWAAAAAAAA MEME-1 width = 15 sites = 7865 llr = 60072 E-value = 1.5e-283 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 799a92579886656 pos.-specific C 1:::::11::::11: probability G 111:17121212232 matrix T ::::::31::11112 bits 2.8 2.6 2.3 2.0 Relative 1.7 Entropy 1.4 * (11.0 bits) 1.1 **** * 0.9 ***** ** 0.6 ****** ***** 0.3 ****** ******** 0.0 --------------- Multilevel AAAAAGAAAAAAAAA consensus T G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1806443 bayes= 9.87855 E= 1.5e-283 94 -3 -11 -317 130 -195 -138 -414 138 -514 -138 -988 140 -301 -216 -915 136 -777 -89 -1047 -94 -173 241 -355 59 -78 -72 -30 93 -80 34 -271 130 -1959 -45 -492 112 -192 20 -439 118 -152 -74 -285 85 -334 83 -200 82 -84 48 -198 55 -42 86 -165 81 -163 27 -122 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7865 E= 1.5e-283 0.694596 0.136427 0.128798 0.040178 0.890019 0.036109 0.053401 0.020470 0.942276 0.003942 0.053401 0.000381 0.950922 0.017292 0.031151 0.000636 0.924221 0.000636 0.074889 0.000254 0.187794 0.041958 0.739479 0.030769 0.542022 0.080992 0.084425 0.292562 0.689002 0.080102 0.175842 0.055054 0.885950 0.000000 0.102098 0.011952 0.786395 0.036872 0.159568 0.017165 0.818055 0.048697 0.083153 0.050095 0.648697 0.013732 0.247425 0.090146 0.637127 0.077686 0.194024 0.091163 0.527654 0.104387 0.253020 0.114940 0.633058 0.044882 0.167705 0.154355 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAGWAAAAAAAA MEME-1 regular expression -------------------------------------------------------------------------------- AAAAAG[AT]AAAA[AG]A[AG]A -------------------------------------------------------------------------------- Time 76.55 secs. ******************************************************************************** ******************************************************************************** MOTIF AVAAAAAG MEME-2 width = 8 sites = 7928 llr = 50701 E-value = 9.1e-061 ******************************************************************************** -------------------------------------------------------------------------------- Motif AVAAAAAG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5489aaa: pos.-specific C 121::::: probability G 231::::a matrix T 21:::::: bits 2.8 * 2.6 * 2.3 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.2 bits) 1.1 ***** 0.9 ***** 0.6 ****** 0.3 ******** 0.0 -------- Multilevel AAAAAAAG consensus G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAAAG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 1861981 bayes= 9.91282 E= 9.1e-061 59 -32 28 -105 8 72 103 -176 112 -23 -133 -303 136 -1960 -253 -287 146 -652 -506 -1960 147 -1011 -1960 -1960 147 -1960 -679 -1960 -497 -1960 283 -890 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAAAG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 7928 E= 9.1e-061 0.544652 0.111756 0.168895 0.174697 0.380298 0.228683 0.284561 0.106458 0.781660 0.118567 0.055499 0.044273 0.926715 0.000000 0.024092 0.049193 0.994324 0.001514 0.004162 0.000000 0.999874 0.000126 0.000000 0.000000 0.998739 0.000000 0.001261 0.000000 0.011478 0.000000 0.987765 0.000757 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AVAAAAAG MEME-2 regular expression -------------------------------------------------------------------------------- A[AGC]AAAAAG -------------------------------------------------------------------------------- Time 143.78 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************