******************************************************************************** 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/AT1G25550_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/AT1G25550_peak_sequences.fasta -dna -oc out/AT1G25550 -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= 1104 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= 168569 N= 1104 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.321 C 0.179 G 0.179 T 0.321 Background letter frequencies (from file dataset with add-one prior applied): A 0.322 C 0.178 G 0.178 T 0.322 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RGAATCTTHDATWYH MEME-1 width = 15 sites = 1082 llr = 8551 E-value = 1.8e-593 ******************************************************************************** -------------------------------------------------------------------------------- Motif RGAATCTTHDATWYH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5:9a:2122262312 pos.-specific C 1::::8:24111252 probability G 3a:::::11421112 matrix T 1:::a:963226534 bits 2.5 * 2.2 * 2.0 * 1.7 * Relative 1.5 * *** Entropy 1.2 ****** (11.4 bits) 1.0 ****** 0.7 ****** 0.5 ****** * 0.2 ************ * 0.0 --------------- Multilevel AGAATCTTCGATTCT consensus G A TT AATC sequence AA A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAATCTTHDATWYH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 153113 bayes= 7.92831 E= 1.8e-593 54 -97 96 -175 -1672 -1672 249 -1672 152 -413 -289 -295 161 -1672 -1672 -412 -1672 -658 -1672 163 -47 211 -1672 -1672 -266 -223 -1672 150 -103 4 -97 82 -49 104 -48 -22 -47 -77 126 -44 78 -99 16 -101 -50 -82 -166 93 -31 10 -102 52 -115 148 -77 -33 -56 49 -8 18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAATCTTHDATWYH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1082 E= 1.8e-593 0.467652 0.090573 0.345656 0.096118 0.000000 0.000000 1.000000 0.000000 0.924214 0.010166 0.024030 0.041590 0.981516 0.000000 0.000000 0.018484 0.000000 0.001848 0.000000 0.998152 0.232902 0.767098 0.000000 0.000000 0.050832 0.037893 0.000000 0.911275 0.158041 0.182994 0.090573 0.568392 0.229205 0.365989 0.127542 0.277264 0.232902 0.104436 0.425139 0.237523 0.552680 0.089649 0.197782 0.159889 0.228281 0.100739 0.056377 0.614603 0.260628 0.190388 0.087800 0.461183 0.145102 0.494455 0.104436 0.256007 0.219039 0.248614 0.168207 0.364140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RGAATCTTHDATWYH MEME-1 regular expression -------------------------------------------------------------------------------- [AG]GAAT[CA]TT[CTA][GTA]A[TA][TA][CT][TCA] -------------------------------------------------------------------------------- Time 127.49 secs. ******************************************************************************** ******************************************************************************** MOTIF TTYTTCTYYTTCTTYTTYTTB MEME-2 width = 21 sites = 232 llr = 2330 E-value = 9.0e-035 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTYTTCTYYTTCTTYTTYTTB MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::1:11::2::3:1:::1:: pos.-specific C 235226:44217115116224 probability G 1::11:::11:1:111::122 matrix T 675673965582673884663 bits 2.5 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 * (14.5 bits) 1.0 * ** * ** 0.7 ** ***** ** *** 0.5 ********* ******** ** 0.2 ********************* 0.0 --------------------- Multilevel TTCTTCTTTTTCTTCTTCTTC consensus CTCCT CCC TA T TCCT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTTCTYYTTCTTYTTYTTB MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 146489 bayes= 11.2723 E= 9.0e-035 -147 3 -156 99 -277 68 -1450 105 -1450 152 -278 53 -252 31 -61 91 -1450 22 -119 115 -252 176 -191 -14 -222 -219 -1450 147 -1450 106 -378 93 -1450 116 -97 67 -105 31 -46 62 -290 -61 -256 133 -1450 189 -51 -58 -22 -56 -1450 90 -322 -72 -41 117 -158 155 -112 -16 -305 -56 -156 127 -464 -36 -236 134 -1450 172 -1450 36 -198 28 -61 86 -1450 44 -12 88 -277 128 31 -10 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTTCTYYTTCTTYTTYTTB MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 232 E= 9.0e-035 0.116379 0.181034 0.060345 0.642241 0.047414 0.284483 0.000000 0.668103 0.000000 0.508621 0.025862 0.465517 0.056034 0.219828 0.116379 0.607759 0.000000 0.206897 0.077586 0.715517 0.056034 0.603448 0.047414 0.293103 0.068966 0.038793 0.000000 0.892241 0.000000 0.370690 0.012931 0.616379 0.000000 0.396552 0.090517 0.512931 0.155172 0.219828 0.129310 0.495690 0.043103 0.116379 0.030172 0.810345 0.000000 0.659483 0.125000 0.215517 0.275862 0.120690 0.000000 0.603448 0.034483 0.107759 0.133621 0.724138 0.107759 0.521552 0.081897 0.288793 0.038793 0.120690 0.060345 0.780172 0.012931 0.137931 0.034483 0.814655 0.000000 0.586207 0.000000 0.413793 0.081897 0.215517 0.116379 0.586207 0.000000 0.241379 0.163793 0.594828 0.047414 0.431034 0.219828 0.301724 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTTCTYYTTCTTYTTYTTB MEME-2 regular expression -------------------------------------------------------------------------------- T[TC][CT][TC][TC][CT]T[TC][TC][TC]T[CT][TA]T[CT]TT[CT][TC][TC][CTG] -------------------------------------------------------------------------------- Time 234.48 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************