******************************************************************************** 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/AT5G60850_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/AT5G60850_peak_sequences.fasta -dna -oc out/AT5G60850 -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= 6418 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= 1724497 N= 6418 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 AAAAAAAAAAAAAAG MEME-1 width = 15 sites = 6379 llr = 47623 E-value = 4.0e-188 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 66767777579aaa1 pos.-specific C 1111111111::::: probability G 2112122221::::8 matrix T 11111:11111:::: bits 2.9 2.6 2.3 2.0 * Relative 1.7 * Entropy 1.4 * ** (10.8 bits) 1.1 **** 0.9 ***** 0.6 *** ****** 0.3 *************** 0.0 --------------- Multilevel AAAAAAAAAAAAAAG consensus G G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1634645 bayes= 10.0173 E= 4.0e-188 68 -44 35 -133 79 3 4 -201 90 -87 -7 -163 73 -33 63 -228 103 -54 -47 -246 104 -118 13 -308 92 -112 37 -232 90 -79 28 -225 52 10 69 -172 101 -134 9 -233 125 -190 -166 -261 147 -1928 -1928 -1928 142 -352 -277 -665 144 -1928 -293 -836 -133 -1928 261 -489 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6379 E= 4.0e-188 0.577677 0.102054 0.176203 0.144066 0.626901 0.141088 0.142029 0.089983 0.675654 0.076031 0.131839 0.116476 0.601035 0.109892 0.214767 0.074306 0.738517 0.095626 0.100329 0.065528 0.744474 0.061295 0.151434 0.042797 0.684904 0.063646 0.179182 0.072268 0.675811 0.080420 0.167895 0.075874 0.517793 0.148769 0.223860 0.109578 0.725976 0.054868 0.147202 0.071955 0.859853 0.037153 0.043894 0.059100 1.000000 0.000000 0.000000 0.000000 0.963944 0.012071 0.020379 0.003606 0.980718 0.000000 0.018185 0.001097 0.143753 0.000000 0.844019 0.012228 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAAAAAAAAAAAG MEME-1 regular expression -------------------------------------------------------------------------------- AAA[AG]AAAA[AG]AAAAAG -------------------------------------------------------------------------------- Time 67.75 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTHMCTTTTT MEME-2 width = 11 sites = 6308 llr = 43193 E-value = 7.5e-089 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTHMCTTTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 21136::::11 pos.-specific C 11223a::::1 probability G 12111:::::1 matrix T 66641:aaa97 bits 2.9 * 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 TTTTACTTTTT consensus A AC sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTHMCTTTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1660317 bayes= 10.1437 E= 7.5e-089 -54 -103 -29 66 -156 -47 28 75 -134 44 -104 74 -13 70 -102 6 63 101 -102 -195 -1927 285 -1927 -1927 -1927 -977 -1927 147 -1927 -977 -1927 147 -1927 -1927 -1927 147 -278 -364 -1927 137 -220 3 -52 92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTHMCTTTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 6308 E= 7.5e-089 0.248890 0.068009 0.113507 0.569594 0.122543 0.100032 0.167882 0.609543 0.142359 0.188174 0.067375 0.602093 0.330216 0.225587 0.068484 0.375713 0.558814 0.279486 0.068167 0.093532 0.000000 1.000000 0.000000 0.000000 0.000000 0.000159 0.000000 0.999841 0.000000 0.000159 0.000000 0.999841 0.000000 0.000000 0.000000 1.000000 0.052790 0.011097 0.000000 0.936113 0.078630 0.141249 0.096386 0.683735 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTHMCTTTTT MEME-2 regular expression -------------------------------------------------------------------------------- [TA]TT[TAC][AC]CTTTTT -------------------------------------------------------------------------------- Time 133.51 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************