******************************************************************************** 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/AT3G28920_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/AT3G28920_peak_sequences.fasta -dna -oc out/AT3G28920 -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= 6039 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= 1582331 N= 6039 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.386 C 0.114 G 0.114 T 0.386 Background letter frequencies (from file dataset with add-one prior applied): A 0.386 C 0.114 G 0.114 T 0.386 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RGMDNDRGDBRKNBVGDRKRVNSRVDDDG MEME-1 width = 29 sites = 518 llr = 5796 E-value = 3.7e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGMDNDRGDBRKNBVGDRKRVNSRVDDDG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 52523332315:32324313421533221 pos.-specific C :332212213122222:11:343131111 probability G 56143344423533452456224434346 matrix T 1:122312241323124232222:13422 bits 3.1 2.8 2.5 2.2 Relative 1.9 Entropy 1.6 (16.1 bits) 1.3 * * 0.9 ** * * * * 0.6 ** ** * ** *** **** * 0.3 ***************************** 0.0 ----------------------------- Multilevel GGAGGGGGGTAGATGGAGGGACGAGGTGG consensus ACCAAAACACGTGGAATATACGCGAAGAT sequence T T TG CCC GT GA CTAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGMDNDRGDBRKNBVGDRKRVNSRVDDDG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 1413238 bayes= 13.5675 E= 3.7e-004 23 -163 202 -294 -112 123 229 -1566 32 135 -7 -169 -77 41 181 -79 -37 69 159 -114 -29 -63 160 -54 -39 42 194 -174 -127 91 193 -102 -60 -24 182 -64 -138 123 100 -11 43 5 126 -209 -764 75 205 -20 -24 107 124 -122 -134 86 145 -23 -33 91 179 -215 -81 48 200 -122 6 -1566 109 -11 -59 -49 196 -81 -189 29 201 -37 -46 -1566 229 -124 -11 119 99 -130 -81 167 103 -106 -140 118 192 -122 28 -21 193 -1566 -42 125 158 -194 -58 23 163 -59 -76 -42 116 16 -66 3 184 -74 -274 23 238 -84 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGMDNDRGDBRKNBVGDRKRVNSRVDDDG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 518 E= 3.7e-004 0.451737 0.036680 0.461390 0.050193 0.177606 0.266409 0.555985 0.000000 0.482625 0.289575 0.108108 0.119691 0.225869 0.150579 0.399614 0.223938 0.299228 0.183398 0.341699 0.175676 0.316602 0.073359 0.343629 0.266409 0.295367 0.152510 0.436293 0.115830 0.160232 0.214286 0.434363 0.191120 0.254826 0.096525 0.401544 0.247104 0.148649 0.266409 0.227799 0.357143 0.519305 0.117761 0.272201 0.090734 0.001931 0.191120 0.471042 0.335907 0.326255 0.239382 0.268340 0.166023 0.152510 0.206564 0.310811 0.330116 0.306950 0.214286 0.391892 0.086873 0.220077 0.158301 0.455598 0.166023 0.401544 0.000000 0.241313 0.357143 0.256757 0.081081 0.442085 0.220077 0.104247 0.138996 0.457529 0.299228 0.279923 0.000000 0.555985 0.164093 0.359073 0.258687 0.225869 0.156371 0.220077 0.362934 0.231660 0.185328 0.146718 0.256757 0.430502 0.166023 0.469112 0.098456 0.432432 0.000000 0.289575 0.270270 0.339768 0.100386 0.258687 0.133205 0.351351 0.256757 0.227799 0.084942 0.254826 0.432432 0.245174 0.115830 0.407336 0.231660 0.057915 0.133205 0.592664 0.216216 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGMDNDRGDBRKNBVGDRKRVNSRVDDDG MEME-1 regular expression -------------------------------------------------------------------------------- [GA][GC][AC][GAT][GA][GAT][GA][GC][GAT][TCG][AG][GT][AGC][TGC][GAC][GA][ATG][GAT][GT][GA][ACG][CGA][GC][AG][GAC][GAT][TGA][GAT][GT] -------------------------------------------------------------------------------- Time 70.80 secs. ******************************************************************************** ******************************************************************************** MOTIF ATGKYGGTTTGRRTTTACAAADGAGAATTAGGGTTTAGATT MEME-2 width = 41 sites = 14 llr = 587 E-value = 1.4e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif ATGKYGGTTTGRRTTTACAAADGAGAATTAGGGTTTAGATT MEME-2 Description -------------------------------------------------------------------------------- Simplified A a:21:11:1:1441::91aaa338:8a::9:21:::9:9:: pos.-specific C ::::61:::::::::1:7::::::::::::1:::::::::: probability G ::84:89:::966:::1::::47:a2:1::989::::a::: matrix T :a:54::a9a:1:9a9:2:::4:2:::9a11::aaa1:1aa bits 3.1 * * 2.8 * * 2.5 * * * 2.2 * * * * * * Relative 1.9 * ** * * * *** * Entropy 1.6 * ** * * * * *** * (60.5 bits) 1.3 *** **** **** ******* * * *** ****** * ** 0.9 *** ***************** * ***************** 0.6 ********************* ******************* 0.3 ***************************************** 0.0 ----------------------------------------- Multilevel ATGTCGGTTTGGGTTTACAAAGGAGAATTAGGGTTTAGATT consensus AGT AA T TAT G A sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGKYGGTTTGRRTTTACAAADGAGAATTAGGGTTTAGATT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 41 n= 1340770 bayes= 17.7697 E= 1.4e-001 137 -1045 -1045 -1045 -1045 -1045 -1045 137 -85 -1045 279 -1045 -143 -1045 165 37 -1045 233 -1045 15 -143 -67 279 -1045 -143 -1045 291 -1045 -1045 -1045 -1045 137 -243 -1045 -1045 126 -1045 -1045 -1045 137 -143 -1045 291 -1045 -11 -1045 233 -243 15 -1045 233 -1045 -243 -1045 -1045 126 -1045 -1045 -1045 137 -1045 -67 -1045 126 126 -1045 -67 -1045 -243 265 -1045 -85 137 -1045 -1045 -1045 137 -1045 -1045 -1045 137 -1045 -1045 -1045 -43 -1045 165 -11 -43 -1045 265 -1045 102 -1045 -1045 -85 -1045 -1045 314 -1045 102 -1045 91 -1045 137 -1045 -1045 -1045 -1045 -1045 -67 126 -1045 -1045 -1045 137 126 -1045 -1045 -243 -1045 -67 291 -243 -85 -1045 279 -1045 -243 -1045 303 -1045 -1045 -1045 -1045 137 -1045 -1045 -1045 137 -1045 -1045 -1045 137 126 -1045 -1045 -243 -1045 -1045 314 -1045 126 -1045 -1045 -243 -1045 -1045 -1045 137 -1045 -1045 -1045 137 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGKYGGTTTGRRTTTACAAADGAGAATTAGGGTTTAGATT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 41 nsites= 14 E= 1.4e-001 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.214286 0.000000 0.785714 0.000000 0.142857 0.000000 0.357143 0.500000 0.000000 0.571429 0.000000 0.428571 0.142857 0.071429 0.785714 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 0.071429 0.000000 0.000000 0.928571 0.000000 0.000000 0.000000 1.000000 0.142857 0.000000 0.857143 0.000000 0.357143 0.000000 0.571429 0.071429 0.428571 0.000000 0.571429 0.000000 0.071429 0.000000 0.000000 0.928571 0.000000 0.000000 0.000000 1.000000 0.000000 0.071429 0.000000 0.928571 0.928571 0.000000 0.071429 0.000000 0.071429 0.714286 0.000000 0.214286 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.285714 0.000000 0.357143 0.357143 0.285714 0.000000 0.714286 0.000000 0.785714 0.000000 0.000000 0.214286 0.000000 0.000000 1.000000 0.000000 0.785714 0.000000 0.214286 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.071429 0.928571 0.000000 0.000000 0.000000 1.000000 0.928571 0.000000 0.000000 0.071429 0.000000 0.071429 0.857143 0.071429 0.214286 0.000000 0.785714 0.000000 0.071429 0.000000 0.928571 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.928571 0.000000 0.000000 0.071429 0.000000 0.000000 1.000000 0.000000 0.928571 0.000000 0.000000 0.071429 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ATGKYGGTTTGRRTTTACAAADGAGAATTAGGGTTTAGATT MEME-2 regular expression -------------------------------------------------------------------------------- AT[GA][TG][CT]GGTTTG[GA][GA]TTTA[CT]AAA[GTA][GA][AT]G[AG]ATTAG[GA]GTTTAGATT -------------------------------------------------------------------------------- Time 136.93 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************