******************************************************************************** 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/AT5G19790_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/AT5G19790_peak_sequences.fasta -dna -oc out/AT5G19790 -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= 5487 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= 1192413 N= 5487 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.262 C 0.238 G 0.238 T 0.262 Background letter frequencies (from file dataset with add-one prior applied): A 0.263 C 0.237 G 0.237 T 0.263 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF MGVCGGCGRHRRHRD MEME-1 width = 15 sites = 5484 llr = 42123 E-value = 6.9e-319 ******************************************************************************** -------------------------------------------------------------------------------- Motif MGVCGGCGRHRRHRD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 313:::125434333 pos.-specific C 4:4a::811211311 probability G 293:aa:64154143 matrix T 1::::::11222322 bits 2.1 ** 1.9 *** 1.7 * *** 1.5 * *** Relative 1.2 * **** Entropy 1.0 * **** (11.1 bits) 0.8 * **** 0.6 * **** 0.4 ******** 0.2 ************ * 0.0 --------------- Multilevel CGCCGGCGAAGGAGA consensus A A GCAACAG sequence G T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGVCGGCGRHRRHRD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1115595 bayes= 9.58447 E= 6.9e-319 14 83 -30 -141 -212 -1906 198 -500 11 78 25 -334 -429 206 -1906 -1906 -1049 -1906 206 -461 -949 -1906 208 -1049 -123 183 -1906 -253 -44 -87 124 -116 79 -155 67 -161 68 4 -137 -12 -2 -193 103 -42 42 -127 64 -54 30 21 -71 -2 15 -99 74 -43 39 -70 49 -58 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGVCGGCGRHRRHRD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5484 E= 6.9e-319 0.289387 0.419767 0.191831 0.099015 0.060722 0.000000 0.931072 0.008206 0.284646 0.407549 0.281729 0.026076 0.013494 0.986506 0.000000 0.000000 0.000182 0.000000 0.989059 0.010759 0.000365 0.000000 0.999453 0.000182 0.112327 0.842086 0.000000 0.045587 0.193472 0.129468 0.559446 0.117615 0.454960 0.080780 0.378009 0.086251 0.423049 0.243800 0.091357 0.241794 0.258753 0.061999 0.482130 0.197119 0.353027 0.097921 0.367797 0.181255 0.322939 0.273158 0.145150 0.258753 0.291028 0.119074 0.394420 0.195478 0.345551 0.145332 0.332604 0.176513 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif MGVCGGCGRHRRHRD MEME-1 regular expression -------------------------------------------------------------------------------- [CA]G[CAG]CGGCG[AG][ACT][GA][GA][ACT][GA][AG] -------------------------------------------------------------------------------- Time 69.50 secs. ******************************************************************************** ******************************************************************************** MOTIF RRARRARRARGARRARRARGA MEME-2 width = 21 sites = 1387 llr = 14679 E-value = 1.6e-089 ******************************************************************************** -------------------------------------------------------------------------------- Motif RRARRARRARGARRARRARGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 447537448637537446537 pos.-specific C ::2:::1::1:1:1:1:11:1 probability G 56147:562361461462361 matrix T 1:11:21::::11:1::11:1 bits 2.1 1.9 1.7 1.5 Relative 1.2 Entropy 1.0 * ** ** * (15.3 bits) 0.8 * ** ** * ** * * 0.6 ****** ******** * * 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GGAAGAGGAAGAAGAAGAAGA consensus AA GATAA GA GA GAGGA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRARRARRARGARRARRARGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1082673 bayes= 11.8971 E= 1.6e-089 71 -1708 96 -127 42 -1708 145 -851 136 -53 -124 -219 80 -290 91 -199 36 -1708 149 -1708 150 -272 -677 -26 49 -192 105 -176 47 -836 142 -1708 159 -1708 -33 -370 114 -217 46 -276 8 -260 145 -293 148 -134 -107 -219 90 -1708 67 -101 35 -182 133 -1708 150 -377 -72 -149 77 -86 65 -240 69 -1708 128 -751 116 -146 2 -159 101 -144 30 -150 27 -836 144 -276 132 -138 -85 -110 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRARRARRARGARRARRARGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1387 E= 1.6e-089 0.431146 0.000000 0.459986 0.108868 0.351118 0.000000 0.648161 0.000721 0.677722 0.164384 0.100216 0.057678 0.457823 0.031723 0.444124 0.066330 0.336698 0.000000 0.663302 0.000000 0.741889 0.036049 0.002163 0.219899 0.368421 0.062725 0.490988 0.077866 0.365537 0.000721 0.633742 0.000000 0.790916 0.000000 0.188897 0.020187 0.581831 0.052632 0.326604 0.038933 0.278298 0.038933 0.648161 0.034607 0.736121 0.093727 0.112473 0.057678 0.491709 0.000000 0.377794 0.130497 0.335977 0.067051 0.596972 0.000000 0.745494 0.017304 0.143475 0.093727 0.449171 0.130497 0.370584 0.049748 0.425379 0.000000 0.573180 0.001442 0.586878 0.085797 0.240087 0.087239 0.529200 0.087239 0.290555 0.093006 0.317952 0.000721 0.642394 0.038933 0.655371 0.090844 0.131218 0.122567 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRARRARRARGARRARRARGA MEME-2 regular expression -------------------------------------------------------------------------------- [GA][GA]A[AG][GA][AT][GA][GA]A[AG][GA]A[AG][GA]A[AG][GA][AG][AG][GA]A -------------------------------------------------------------------------------- Time 133.39 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************