******************************************************************************** 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/AT4G10350_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/AT4G10350_peak_sequences.fasta -dna -oc out/AT4G10350 -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= 7984 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= 1617888 N= 7984 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.324 C 0.176 G 0.176 T 0.324 Background letter frequencies (from file dataset with add-one prior applied): A 0.325 C 0.175 G 0.175 T 0.325 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTTNWWHYWYAMGYW MEME-1 width = 15 sites = 7982 llr = 53702 E-value = 8.6e-190 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTTNWWHYWYAMGYW MEME-1 Description -------------------------------------------------------------------------------- Simplified A :::233222:95:14 pos.-specific C 9::3222325:5:32 probability G :3:3111111::71: matrix T 17a2444544::244 bits 2.5 2.3 2.0 * 1.8 * Relative 1.5 * * Entropy 1.3 * * * * (9.7 bits) 1.0 *** *** 0.8 *** **** 0.5 *** **** 0.3 **** * ****** 0.0 --------------- Multilevel CTTGTTTTTCAAGTA consensus G CAACCAT CTCT sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTNWWHYWYAMGYW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1506112 bayes= 9.87737 E= 8.6e-190 -446 240 -499 -251 -644 -580 60 116 -602 -569 -564 160 -91 63 96 -58 -4 -10 -39 25 -9 -3 -58 32 -52 51 -34 25 -99 57 -82 56 -44 10 -32 41 -450 139 -57 34 154 -192 -580 -621 68 144 -559 -630 -392 -549 208 -45 -114 97 -62 29 32 11 -540 30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTNWWHYWYAMGYW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7982 E= 8.6e-190 0.014783 0.922451 0.005512 0.057254 0.003758 0.003132 0.265347 0.727762 0.005011 0.003383 0.003508 0.988098 0.172638 0.270484 0.338512 0.218366 0.316211 0.162491 0.133550 0.387747 0.306565 0.171511 0.116888 0.405036 0.227637 0.248434 0.137685 0.386244 0.164245 0.258457 0.099223 0.478076 0.240666 0.186545 0.140316 0.432473 0.014407 0.456151 0.117264 0.412177 0.946379 0.046104 0.003132 0.004385 0.519669 0.472563 0.003633 0.004134 0.021423 0.003884 0.737159 0.237534 0.147582 0.341268 0.113255 0.397895 0.405287 0.188675 0.004134 0.401904 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTTNWWHYWYAMGYW MEME-1 regular expression -------------------------------------------------------------------------------- C[TG]T[GCT][TA][TA][TCA][TC][TA][CT]A[AC][GT][TC][AT] -------------------------------------------------------------------------------- Time 84.93 secs. ******************************************************************************** ******************************************************************************** MOTIF RARAARAARAAAAAR MEME-2 width = 15 sites = 2177 llr = 19778 E-value = 1.1e-022 ******************************************************************************** -------------------------------------------------------------------------------- Motif RARAARAARAAAAAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 586975895a66786 pos.-specific C 21::12:1::21:1: probability G 3141242:5:22314 matrix T ::::::::::::::: bits 2.5 2.3 2.0 1.8 Relative 1.5 * Entropy 1.3 * * * (13.1 bits) 1.0 * **** * 0.8 *** **** **** 0.5 *************** 0.3 *************** 0.0 --------------- Multilevel AAAAAAAAGAAAAAA consensus G G GG A CGG G sequence C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAARAARAAAAAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1506112 bayes= 11.714 E= 1.1e-022 59 26 77 -688 121 -88 -70 -282 83 -228 114 -1773 143 -1773 -48 -1773 113 -179 40 -530 50 -14 105 -398 137 -1773 -12 -1773 153 -160 -1773 -1773 55 -448 157 -1773 157 -1773 -246 -1773 80 38 -10 -288 99 -77 52 -1773 109 -321 74 -1773 126 -47 -85 -1773 79 -698 124 -380 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAARAARAAAAAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 2177 E= 1.1e-022 0.491043 0.208544 0.297657 0.002756 0.751952 0.094626 0.107487 0.045935 0.580156 0.035829 0.384015 0.000000 0.874598 0.000000 0.125402 0.000000 0.710152 0.050528 0.231052 0.008268 0.459807 0.158934 0.360588 0.020671 0.839228 0.000000 0.160772 0.000000 0.942582 0.057418 0.000000 0.000000 0.474966 0.007809 0.517226 0.000000 0.968305 0.000000 0.031695 0.000000 0.565457 0.227377 0.163068 0.044097 0.647680 0.102435 0.249885 0.000000 0.690400 0.018833 0.290767 0.000000 0.776757 0.126321 0.096922 0.000000 0.563160 0.001378 0.412035 0.023427 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAARAARAAAAAR MEME-2 regular expression -------------------------------------------------------------------------------- [AGC]A[AG]A[AG][AG]AA[GA]A[AC][AG][AG]A[AG] -------------------------------------------------------------------------------- Time 157.93 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************