******************************************************************************** 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/AT4G01280_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/AT4G01280_peak_sequences.fasta -dna -oc out/AT4G01280 -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= 8654 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= 2339282 N= 8654 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.367 C 0.133 G 0.133 T 0.367 Background letter frequencies (from file dataset with add-one prior applied): A 0.368 C 0.132 G 0.132 T 0.368 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AGATWTTTTTT MEME-1 width = 11 sites = 8610 llr = 64728 E-value = 9.7e-177 ******************************************************************************** -------------------------------------------------------------------------------- Motif AGATWTTTTTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 7:a:6::1122 pos.-specific C ::::::::111 probability G 1a::::::112 matrix T 2::a4aa9765 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.8 * Entropy 1.5 *** ** (10.8 bits) 1.2 *** ** 0.9 *** *** 0.6 *** *** 0.3 ********** 0.0 ----------- Multilevel AGATATTTTTT consensus T A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATWTTTTTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2252740 bayes= 10.133 E= 9.7e-177 97 -329 -54 -106 -1063 -1972 292 -931 144 -1972 -1972 -1972 -1162 -1972 -1972 144 72 -303 -1972 4 -904 -915 -634 144 -831 -857 -381 143 -227 -283 -346 128 -131 -88 -70 93 -117 11 1 61 -79 17 42 33 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATWTTTTTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 8610 E= 9.7e-177 0.719396 0.013473 0.090941 0.176190 0.000232 0.000000 0.999187 0.000581 1.000000 0.000000 0.000000 0.000000 0.000116 0.000000 0.000000 0.999884 0.606156 0.016144 0.000000 0.377700 0.000697 0.000232 0.001626 0.997445 0.001161 0.000348 0.009408 0.989082 0.076423 0.018583 0.011963 0.893031 0.148432 0.071893 0.081069 0.698606 0.163995 0.142276 0.132985 0.560743 0.212311 0.148897 0.177120 0.461672 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AGATWTTTTTT MEME-1 regular expression -------------------------------------------------------------------------------- AGAT[AT]TTTTT[TA] -------------------------------------------------------------------------------- Time 78.44 secs. ******************************************************************************** ******************************************************************************** MOTIF GARAAARARARARARAAAAAR MEME-2 width = 21 sites = 829 llr = 9488 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GARAAARARARARARAAAAAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A :65979676968596887695 pos.-specific C 312:1:::::::1:::1:1:1 probability G 623121423132314213313 matrix T 11:::::11:1:1::::1::1 bits 2.9 2.6 2.3 2.0 Relative 1.8 Entropy 1.5 (16.5 bits) 1.2 * ** * * * 0.9 * **** * * **** * 0.6 * ****************** 0.3 ********************* 0.0 --------------------- Multilevel GAAAAAAAAAAAAAAAAAAAA consensus C G G G G G G G GG G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARAAARARARARARAAAAAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2166200 bayes= 13.6187 E= 1.5e-004 -544 95 215 -130 76 -27 37 -193 49 38 119 -525 122 -1634 -16 -393 89 -67 83 -1634 134 -1634 -122 -467 78 -1634 149 -1634 100 -360 58 -270 60 -145 124 -214 128 -207 -87 -1634 68 -1634 139 -255 110 -319 56 -1634 58 -77 121 -245 121 -202 -92 -308 76 -1634 152 -1634 110 -192 39 -1634 117 -92 -33 -1634 82 -1634 106 -232 75 -107 106 -312 126 -1634 -16 -1634 34 -47 129 -165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARAAARARARARARAAAAAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 829 E= 1.5e-004 0.008444 0.254524 0.587455 0.149578 0.622437 0.109771 0.171291 0.096502 0.517491 0.172497 0.300362 0.009650 0.857660 0.000000 0.118215 0.024125 0.681544 0.083233 0.235223 0.000000 0.928830 0.000000 0.056695 0.014475 0.629674 0.000000 0.370326 0.000000 0.734620 0.010856 0.197829 0.056695 0.557298 0.048251 0.311218 0.083233 0.896261 0.031363 0.072376 0.000000 0.589867 0.000000 0.347407 0.062726 0.791315 0.014475 0.194210 0.000000 0.548854 0.077201 0.306393 0.067551 0.854041 0.032569 0.069964 0.043426 0.622437 0.000000 0.377563 0.000000 0.791315 0.034982 0.173703 0.000000 0.825090 0.069964 0.104946 0.000000 0.650181 0.000000 0.276236 0.073583 0.618818 0.062726 0.276236 0.042220 0.881785 0.000000 0.118215 0.000000 0.465621 0.095296 0.322075 0.117008 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GARAAARARARARARAAAAAR MEME-2 regular expression -------------------------------------------------------------------------------- [GC]A[AG]A[AG]A[AG]A[AG]A[AG]A[AG]A[AG]AA[AG][AG]A[AG] -------------------------------------------------------------------------------- Time 147.87 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************