******************************************************************************** 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/AT5G53950_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/AT5G53950_peak_sequences.fasta -dna -oc out/AT5G53950 -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= 4021 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= 855109 N= 4021 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.325 C 0.175 G 0.175 T 0.325 Background letter frequencies (from file dataset with add-one prior applied): A 0.326 C 0.174 G 0.174 T 0.326 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTNCTTSTWHNWCAMGYWAHY MEME-1 width = 21 sites = 3964 llr = 30296 E-value = 1.8e-308 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTNCTTSTWHNWCAMGYWAHY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2231:12232241a4114722 pos.-specific C 11281:2223316:6:32:44 probability G :22:2:4112211::81::11 matrix T 8531792544333::154332 bits 2.5 2.3 2.0 1.8 Relative 1.5 * * Entropy 1.3 * *** (11.0 bits) 1.0 * * *** 0.8 *** **** 0.5 * *** **** * 0.3 ** ***** ********* 0.0 --------------------- Multilevel TTTCTTGTTTTACACGTAACC consensus AA G CAACCTT A CTTTT sequence G C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTSTWHNWCAMGYWAHY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 774689 bayes= 9.84059 E= 1.8e-308 -94 -161 -334 121 -51 -152 6 70 -16 -2 40 -9 -154 218 -289 -209 -653 -130 50 106 -154 -426 -259 138 -76 42 124 -100 -56 16 -104 62 -33 15 -34 34 -83 76 -12 15 -71 76 6 -1 45 -39 -48 -13 -254 181 -163 -23 162 -1860 -1860 -1860 31 178 -1860 -933 -219 -1860 224 -162 -125 86 -86 47 31 20 -283 19 111 -326 -330 -32 -65 114 -110 1 -71 136 -57 -46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTSTWHNWCAMGYWAHY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 3964 E= 1.8e-308 0.170283 0.057013 0.017154 0.755550 0.229566 0.060797 0.181635 0.528002 0.291120 0.172048 0.230071 0.306761 0.111756 0.788345 0.023461 0.076438 0.003532 0.070636 0.246468 0.679364 0.111756 0.009082 0.029011 0.850151 0.192735 0.232593 0.411705 0.162967 0.221493 0.195005 0.084511 0.498991 0.258325 0.193239 0.137235 0.411201 0.183653 0.294147 0.160192 0.362008 0.198537 0.295409 0.182139 0.323915 0.445257 0.132947 0.124874 0.296922 0.056004 0.609738 0.056256 0.278002 1.000000 0.000000 0.000000 0.000000 0.403128 0.596367 0.000000 0.000505 0.071393 0.000000 0.822402 0.106206 0.136983 0.316599 0.096115 0.450303 0.404390 0.200050 0.024470 0.371090 0.702321 0.018163 0.017659 0.261857 0.207871 0.382947 0.081231 0.327952 0.199798 0.445762 0.117053 0.237386 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTNCTTSTWHNWCAMGYWAHY MEME-1 regular expression -------------------------------------------------------------------------------- T[TA][TAG]C[TG]T[GC][TA][TA][TC][TC][AT][CT]A[CA]G[TC][ATC][AT][CTA][CT] -------------------------------------------------------------------------------- Time 80.25 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARAARAARARAAARAARAR MEME-2 width = 21 sites = 690 llr = 7085 E-value = 2.5e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARAARAARARAAARAARAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 466488588585788488564 pos.-specific C 1111:::1:112::::2:112 probability G 3125225:14:33225:1423 matrix T 221:::::::11:::1:::11 bits 2.5 2.3 2.0 1.8 Relative 1.5 Entropy 1.3 (14.8 bits) 1.0 ***** *** ** 0.8 ******** *** *** 0.5 ******** ******* 0.3 ********************* 0.0 --------------------- Multilevel AAAGAAAAAAAAAAAGAAAAA consensus G A GG G GG GA GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARARAAARAARAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 774689 bayes= 12.2089 E= 2.5e-032 13 -25 95 -102 79 -59 -31 -87 84 -40 -9 -144 23 -52 151 -1607 133 -1607 -17 -356 124 -432 36 -1607 70 -1607 138 -435 137 -35 -1607 -411 136 -186 -59 -1607 55 -59 123 -1607 130 -59 -310 -239 64 2 57 -253 101 -321 90 -1607 129 -1607 7 -411 122 -1607 47 -1607 33 -291 141 -164 132 8 -1607 -1607 137 -491 -40 -400 74 -108 110 -1607 86 -40 23 -220 27 -4 73 -114 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARARAAARAARAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 690 E= 2.5e-032 0.356522 0.146377 0.336232 0.160870 0.565217 0.115942 0.140580 0.178261 0.584058 0.131884 0.163768 0.120290 0.382609 0.121739 0.495652 0.000000 0.817391 0.000000 0.155072 0.027536 0.768116 0.008696 0.223188 0.000000 0.530435 0.000000 0.453623 0.015942 0.844928 0.136232 0.000000 0.018841 0.836232 0.047826 0.115942 0.000000 0.476812 0.115942 0.407246 0.000000 0.801449 0.115942 0.020290 0.062319 0.507246 0.176812 0.259420 0.056522 0.656522 0.018841 0.324638 0.000000 0.798551 0.000000 0.182609 0.018841 0.757971 0.000000 0.242029 0.000000 0.408696 0.023188 0.463768 0.104348 0.815942 0.184058 0.000000 0.000000 0.842029 0.005797 0.131884 0.020290 0.544928 0.082609 0.372464 0.000000 0.592754 0.131884 0.204348 0.071014 0.392754 0.169565 0.289855 0.147826 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAARARAAARAARAR MEME-2 regular expression -------------------------------------------------------------------------------- [AG]AA[GA]A[AG][AG]AA[AG]A[AG][AG]A[AG][GA]AA[AG][AG][AG] -------------------------------------------------------------------------------- Time 146.41 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************