******************************************************************************** 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/AT4G21030_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/AT4G21030_peak_sequences.fasta -dna -oc out/AT4G21030 -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= 2007 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= 314125 N= 2007 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.349 C 0.151 G 0.151 T 0.349 Background letter frequencies (from file dataset with add-one prior applied): A 0.35 C 0.15 G 0.15 T 0.35 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTTTRCCTTTTTBW MEME-1 width = 15 sites = 1970 llr = 16721 E-value = 1.6e-732 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTTRCCTTTTTBW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 222223:::::::23 pos.-specific C 21111:8a::::132 probability G 111114:::::::22 matrix T 5666622:aaaa934 bits 2.7 2.5 * 2.2 * 1.9 * Relative 1.6 **** Entropy 1.4 ****** (12.2 bits) 1.1 ****** 0.8 ******* 0.5 ******** 0.3 ************* 0.0 --------------- Multilevel TTTTTGCCTTTTTTT consensus AA A CA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTRCCTTTTTBW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 286027 bayes= 9.16793 E= 1.6e-732 -63 25 -26 43 -68 0 -89 66 -84 -38 -51 74 -118 -28 -71 85 -106 -70 -53 86 -9 -202 158 -90 -284 236 -475 -97 -1759 271 -1759 -434 -1759 -1759 -1759 151 -1759 -1759 -1759 151 -1759 -1759 -1759 151 -294 -1759 -1759 145 -304 -134 -212 130 -122 97 62 -11 -44 27 14 17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTRCCTTTTTBW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1970 E= 1.6e-732 0.226396 0.177665 0.125381 0.470558 0.217766 0.149746 0.080711 0.551777 0.194924 0.115228 0.105076 0.584772 0.154315 0.123350 0.091878 0.630457 0.167513 0.092386 0.104061 0.636041 0.327919 0.037056 0.447208 0.187817 0.048731 0.767005 0.005584 0.178680 0.000000 0.982741 0.000000 0.017259 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.045685 0.000000 0.000000 0.954315 0.042640 0.059391 0.034518 0.863452 0.150254 0.294416 0.230457 0.324873 0.258883 0.180711 0.165482 0.394924 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTRCCTTTTTBW MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TA]TTT[GA]CCTTTTT[TCG][TA] -------------------------------------------------------------------------------- Time 88.67 secs. ******************************************************************************** ******************************************************************************** MOTIF RAARAARAAAAAAAARAAARR MEME-2 width = 21 sites = 821 llr = 7282 E-value = 2.8e-106 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAARAARAAAAAAAARAAARR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 479568677686569598654 pos.-specific C 21:22:::111111:1:::12 probability G 22:32132131222:412332 matrix T 2:1::1:11::121:::::12 bits 2.7 2.5 2.2 1.9 Relative 1.6 Entropy 1.4 (12.8 bits) 1.1 * * ** 0.8 ** ** ** ***** 0.5 ******* ** ****** 0.3 *********** ******* 0.0 --------------------- Multilevel AAAAAAAAAAAAAAAAAAAAA consensus G G GG G GGG G GGGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAAAAAAAARAAARR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 273985 bayes= 10.5952 E= 2.8e-106 28 3 71 -101 100 -52 39 -1633 136 -594 -255 -226 48 11 117 -500 85 20 12 -331 120 -1633 -27 -233 84 -170 112 -816 90 -199 60 -208 92 -99 -34 -127 85 -99 98 -1633 117 -130 -31 -341 78 -124 59 -166 44 -57 64 -89 89 -145 54 -217 141 -1633 -294 -285 47 -33 140 -1633 138 -1633 -71 -1633 116 -436 49 -816 89 -204 106 -816 54 -47 78 -148 24 27 62 -100 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAAAAAAAARAAARR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 821 E= 2.8e-106 0.426309 0.153471 0.246041 0.174178 0.699147 0.104750 0.196102 0.000000 0.898904 0.002436 0.025579 0.073082 0.489647 0.161998 0.337393 0.010962 0.629720 0.171742 0.163216 0.035323 0.806334 0.000000 0.124239 0.069428 0.627284 0.046285 0.325213 0.001218 0.652862 0.037759 0.226553 0.082826 0.661389 0.075518 0.118149 0.144945 0.629720 0.075518 0.294762 0.000000 0.785627 0.060901 0.120585 0.032887 0.600487 0.063337 0.225335 0.110840 0.476248 0.101096 0.233861 0.188794 0.649208 0.054811 0.218027 0.077954 0.931790 0.000000 0.019488 0.048721 0.485993 0.119367 0.394641 0.000000 0.908648 0.000000 0.091352 0.000000 0.780755 0.007308 0.210719 0.001218 0.649208 0.036541 0.313033 0.001218 0.509135 0.108404 0.257004 0.125457 0.414129 0.180268 0.230207 0.175396 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAARAARAAAAAAAARAAARR MEME-2 regular expression -------------------------------------------------------------------------------- [AG]AA[AG]AA[AG][AG]A[AG]A[AG][AG][AG]A[AG]A[AG][AG][AG][AG] -------------------------------------------------------------------------------- Time 162.86 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************