******************************************************************************** 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/AT5G54230_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/AT5G54230_peak_sequences.fasta -dna -oc out/AT5G54230 -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= 1861 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= 303607 N= 1861 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.342 C 0.158 G 0.158 T 0.342 Background letter frequencies (from file dataset with add-one prior applied): A 0.342 C 0.158 G 0.158 T 0.342 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YYYACCTAMYWWW MEME-1 width = 13 sites = 1796 llr = 14859 E-value = 1.1e-584 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYYACCTAMYWWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 11:a1:2a51333 pos.-specific C 336:8a::45112 probability G 1:1:::::::::1 matrix T 563:::7::4655 bits 2.7 * 2.4 * 2.1 * 1.9 ** Relative 1.6 *** * Entropy 1.3 *** * (11.9 bits) 1.1 *** ** 0.8 **** *** 0.5 ********* 0.3 *********** 0.0 ------------- Multilevel TTCACCTAACTTT consensus CCT A CTAAA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYYACCTAMYWWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 13 n= 281275 bayes= 8.51121 E= 1.1e-584 -191 89 -38 54 -191 92 -198 73 -351 184 -150 3 154 -1745 -534 -1745 -127 242 -390 -1745 -1745 266 -1745 -1745 -52 -286 -498 110 155 -1745 -1745 -1745 65 149 -815 -426 -159 162 -534 22 0 -139 -1745 80 3 -18 -186 45 -13 -6 -92 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYYACCTAMYWWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 13 nsites= 1796 E= 1.1e-584 0.090757 0.292316 0.121381 0.495546 0.091314 0.299555 0.040089 0.569042 0.030067 0.565145 0.055679 0.349109 0.996102 0.000000 0.003898 0.000000 0.141425 0.847996 0.010579 0.000000 0.000000 1.000000 0.000000 0.000000 0.238864 0.021715 0.005011 0.734410 1.000000 0.000000 0.000000 0.000000 0.537862 0.443764 0.000557 0.017817 0.113586 0.485523 0.003898 0.396993 0.342984 0.060134 0.000000 0.596882 0.349666 0.139198 0.043430 0.467706 0.312361 0.152004 0.083519 0.452116 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYYACCTAMYWWW MEME-1 regular expression -------------------------------------------------------------------------------- [TC][TC][CT]ACC[TA]A[AC][CT][TA][TA][TA] -------------------------------------------------------------------------------- Time 76.02 secs. ******************************************************************************** ******************************************************************************** MOTIF TTTTBTTTTTYTTTTTYTTT MEME-2 width = 20 sites = 286 llr = 2920 E-value = 9.7e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTBTTTTTYTTTTTYTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::::11::::11:::1::1 pos.-specific C 22214113223:223:3212 probability G 2:::31::2:::112122:: matrix T 58893787786867695796 bits 2.7 2.4 2.1 1.9 Relative 1.6 Entropy 1.3 * (14.7 bits) 1.1 *** * * * 0.8 **** ****** * * ** 0.5 *************** ** 0.3 ******************** 0.0 -------------------- Multilevel TTTTCTTTTTTTTTTTTTTT consensus CC T C CC CCC C C sequence G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTBTTTTTYTTTTTYTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 268248 bayes= 11.9035 E= 9.7e-002 -244 50 38 57 -1480 46 -391 118 -1480 20 -291 122 -403 -118 -318 138 -1480 132 79 -4 -170 -50 -111 105 -252 -18 -291 119 -344 98 -1480 94 -1480 6 6 97 -1480 41 -1480 121 -1480 109 -191 86 -140 -180 -391 125 -222 55 -111 86 -1480 46 -104 105 -1480 67 -1 79 -561 -350 -104 140 -261 103 -1 44 -1480 17 -4 97 -1480 -74 -1480 140 -152 46 -218 88 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTBTTTTTYTTTTTYTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 286 E= 9.7e-002 0.062937 0.223776 0.206294 0.506993 0.000000 0.216783 0.010490 0.772727 0.000000 0.181818 0.020979 0.797203 0.020979 0.069930 0.017483 0.891608 0.000000 0.395105 0.272727 0.332168 0.104895 0.111888 0.073427 0.709790 0.059441 0.139860 0.020979 0.779720 0.031469 0.311189 0.000000 0.657343 0.000000 0.164336 0.164336 0.671329 0.000000 0.209790 0.000000 0.790210 0.000000 0.335664 0.041958 0.622378 0.129371 0.045455 0.010490 0.814685 0.073427 0.230769 0.073427 0.622378 0.000000 0.216783 0.076923 0.706294 0.000000 0.251748 0.157343 0.590909 0.006993 0.013986 0.076923 0.902098 0.055944 0.321678 0.157343 0.465035 0.000000 0.178322 0.153846 0.667832 0.000000 0.094406 0.000000 0.905594 0.118881 0.216783 0.034965 0.629371 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTBTTTTTYTTTTTYTTT MEME-2 regular expression -------------------------------------------------------------------------------- [TCG][TC]TT[CTG]TT[TC]T[TC][TC]T[TC][TC][TC]T[TC]TT[TC] -------------------------------------------------------------------------------- Time 140.97 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************