******************************************************************************** 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/AT1G29160_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/AT1G29160_peak_sequences.fasta -dna -oc out/AT1G29160 -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= 9621 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= 2565644 N= 9621 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.355 C 0.145 G 0.145 T 0.355 Background letter frequencies (from file dataset with add-one prior applied): A 0.356 C 0.144 G 0.144 T 0.356 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RWAAAAAAARAAAAAARARAAAAAAARWR MEME-1 width = 29 sites = 6765 llr = 64143 E-value = 1.4e-285 ******************************************************************************** -------------------------------------------------------------------------------- Motif RWAAAAAAARAAAAAARARAAAAAAARWR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 45466788856779886646566868464 pos.-specific C 112111::1111:1::1:11111:11111 probability G 31222122142:3:123241222131413 matrix T 2321111:::12:::::2121111:1:31 bits 2.8 2.5 2.2 2.0 Relative 1.7 Entropy 1.4 (13.7 bits) 1.1 * 0.8 ** ***** * 0.6 **** ***** **** 0.3 * ************************** 0.0 ----------------------------- Multilevel AAAAAAAAAAAAAAAAAAAAAAAAAAGAA consensus GTC G G G GGG G G ATG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAAAAAARAAAAAARARAAAAAAARWR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 2296256 bayes= 10.6227 E= 1.4e-285 27 -88 99 -79 56 -112 1 -43 28 57 36 -107 65 -19 34 -140 73 -1 49 -243 94 -44 -42 -177 109 -1937 15 -210 123 -1937 9 -479 118 -119 -13 -1937 56 -92 139 -415 80 -124 37 -141 94 -95 -156 -89 92 -198 91 -427 134 -137 -168 -1937 122 -204 -42 -358 116 -1937 20 -325 78 -134 116 -515 76 -242 56 -116 22 -90 146 -165 71 -30 -24 -100 60 -66 67 -134 72 -30 17 -139 76 -17 28 -193 117 -893 -60 -182 80 -92 82 -284 109 -94 -50 -241 21 -33 158 -304 67 -121 -75 -32 17 5 120 -157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAAAAAARAAAAAARARAAAAAAARWR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 6765 E= 1.4e-285 0.429564 0.078344 0.285440 0.206652 0.524612 0.066223 0.145159 0.264006 0.432225 0.213895 0.184775 0.169106 0.557576 0.126090 0.181523 0.134812 0.589061 0.142646 0.202069 0.066223 0.682040 0.105987 0.107465 0.104508 0.757576 0.000000 0.159350 0.083075 0.833703 0.000000 0.153437 0.012860 0.805322 0.062971 0.131707 0.000000 0.526534 0.075831 0.377531 0.020103 0.619512 0.060902 0.185366 0.134220 0.684701 0.074501 0.048928 0.191870 0.675388 0.036364 0.269771 0.018477 0.899335 0.055728 0.044937 0.000000 0.827347 0.035033 0.107908 0.029712 0.797044 0.000000 0.165558 0.037398 0.612121 0.056911 0.320916 0.010052 0.601035 0.026903 0.212269 0.159793 0.414634 0.077162 0.395122 0.113082 0.583296 0.116925 0.121803 0.177975 0.539246 0.091057 0.228677 0.141020 0.585218 0.116778 0.162010 0.135994 0.604878 0.127716 0.174132 0.093274 0.803991 0.000296 0.094900 0.100813 0.620103 0.076127 0.253954 0.049815 0.756689 0.074797 0.101552 0.066962 0.412860 0.114412 0.429564 0.043163 0.566297 0.062232 0.085735 0.285735 0.400591 0.148707 0.331116 0.119586 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWAAAAAAARAAAAAARARAAAAAAARWR MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][AT][AC]A[AG]AAAA[AG]AA[AG]AAA[AG][AG][AG]A[AG]AAA[AG]A[GA][AT][AG] -------------------------------------------------------------------------------- Time 127.14 secs. ******************************************************************************** ******************************************************************************** MOTIF HMCTTTTT MEME-2 width = 8 sites = 9436 llr = 63500 E-value = 5.0e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif HMCTTTTT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 25:::::: pos.-specific C 43a::::1 probability G 11:::::1 matrix T 31:aaa98 bits 2.8 * 2.5 * 2.2 * 2.0 * Relative 1.7 * Entropy 1.4 **** (9.7 bits) 1.1 ***** 0.8 ****** 0.6 ****** 0.3 ******** 0.0 -------- Multilevel CACTTTTT consensus TC sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HMCTTTTT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 2498297 bayes= 10.2206 E= 5.0e-038 -71 148 -129 -15 49 90 -78 -127 -1985 280 -1985 -971 -1985 -571 -1985 149 -1985 -560 -1985 149 -1985 -1985 -1985 149 -301 -365 -1985 141 -468 -28 -140 119 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HMCTTTTT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 9436 E= 5.0e-038 0.218101 0.401865 0.059029 0.321005 0.500848 0.267910 0.083828 0.147414 0.000000 0.999576 0.000000 0.000424 0.000000 0.002755 0.000000 0.997245 0.000000 0.002967 0.000000 0.997033 0.000000 0.000000 0.000000 1.000000 0.044298 0.011446 0.000000 0.944256 0.013883 0.118588 0.054684 0.812844 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HMCTTTTT MEME-2 regular expression -------------------------------------------------------------------------------- [CTA][AC]CTTTTT -------------------------------------------------------------------------------- Time 240.84 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************