******************************************************************************** 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/AT1G28470_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/AT1G28470_peak_sequences.fasta -dna -oc out/AT1G28470 -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= 4816 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= 1010574 N= 4816 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.317 C 0.183 G 0.183 T 0.317 Background letter frequencies (from file dataset with add-one prior applied): A 0.318 C 0.182 G 0.182 T 0.318 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF RWARCKTRWDRDWSAAGHWAH MEME-1 width = 21 sites = 4741 llr = 41355 E-value = 2.9e-490 ******************************************************************************** -------------------------------------------------------------------------------- Motif RWARCKTRWDRDWSAAGHWAH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34642::3543451a8:4562 pos.-specific C 1::18::11211:3:2:21:3 probability G 5124:5:5124224::a1112 matrix T 252115a:432232:::2422 bits 2.5 2.2 * 2.0 * 1.7 * * * Relative 1.5 * * * * Entropy 1.2 * * * * (12.6 bits) 1.0 *** *** 0.7 *** *** 0.5 **** **** 0.2 ********* * ***** ** 0.0 --------------------- Multilevel GTAACGTGAAGAAGAAGAAAC consensus AATG T ATTAGTC C CTTA sequence G T T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWARCKTRWDRDWSAAGHWAH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 914254 bayes= 9.62924 E= 2.9e-490 -10 -129 132 -86 33 -223 -180 68 81 -312 -2 -40 36 -103 107 -140 -106 212 -1885 -244 -1885 -1885 151 60 -1885 -550 -1885 165 2 -51 149 -295 54 -90 -146 22 23 -20 25 -34 -26 -34 113 -72 30 -29 42 -56 67 -241 -25 -6 -183 78 127 -99 165 -1885 -816 -1885 127 35 -1885 -1885 -539 -1885 243 -435 29 44 -54 -41 53 -103 -125 24 101 -232 -106 -43 -38 94 -12 -42 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWARCKTRWDRDWSAAGHWAH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4741 E= 2.9e-490 0.296562 0.074457 0.453069 0.175912 0.399705 0.038599 0.052310 0.509386 0.558954 0.020882 0.179287 0.240877 0.408564 0.089011 0.381565 0.120861 0.152289 0.788863 0.000000 0.058848 0.000000 0.000000 0.518245 0.481755 0.000000 0.004008 0.000000 0.995992 0.322928 0.127399 0.508543 0.041131 0.464459 0.097237 0.066231 0.372073 0.373339 0.157984 0.216621 0.252057 0.265978 0.143641 0.396541 0.193841 0.391900 0.148070 0.243619 0.216410 0.507699 0.034170 0.152499 0.305632 0.089644 0.311960 0.437882 0.160515 0.999367 0.000000 0.000633 0.000000 0.769247 0.230753 0.000000 0.000000 0.007593 0.000000 0.976798 0.015609 0.389369 0.246994 0.124657 0.238979 0.458342 0.089011 0.076355 0.376292 0.639949 0.036279 0.087112 0.236659 0.245307 0.349293 0.167475 0.237924 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RWARCKTRWDRDWSAAGHWAH MEME-1 regular expression -------------------------------------------------------------------------------- [GA][TA][AT][AG]C[GT]T[GA][AT][ATG][GA][AGT][AT][GC]A[AC]G[ACT][AT][AT][CAT] -------------------------------------------------------------------------------- Time 124.79 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTTYTTCTTYTTYTTYTTYH MEME-2 width = 21 sites = 1025 llr = 10554 E-value = 5.2e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTYTTYTTYH MEME-2 Description -------------------------------------------------------------------------------- Simplified A 212:::::1::1111::1112 pos.-specific C 15:242171262152253242 probability G :212::::::::1::::1:12 matrix T 726658937746748746844 bits 2.5 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 ** * (14.9 bits) 1.0 *** ** * 0.7 ******* **** * 0.5 ******************** 0.2 ******************** 0.0 --------------------- Multilevel TCTTTTTCTTCTTCTTCTTCT consensus TAGCC T CTC T CTC TC sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTYTTYTTYH MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 914254 bayes= 12.035 E= 5.2e-038 -106 -69 -422 119 -132 142 -19 -49 -35 -1665 -85 103 -576 15 35 81 -289 126 -1665 71 -1665 21 -1665 131 -476 -137 -1665 153 -1665 194 -1665 -8 -142 -37 -1665 122 -396 43 -522 120 -1665 162 -1665 47 -137 30 -225 95 -150 -94 -54 107 -252 159 -279 22 -220 -17 -1665 127 -676 40 -245 119 -396 155 -1665 49 -231 54 -94 86 -206 -11 -1665 125 -165 129 -91 17 -52 45 -17 21 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTYTTYTTYH MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1025 E= 5.2e-038 0.152195 0.112195 0.009756 0.725854 0.127805 0.485854 0.159024 0.227317 0.249756 0.000000 0.100488 0.649756 0.005854 0.201951 0.232195 0.560000 0.042927 0.435122 0.000000 0.521951 0.000000 0.209756 0.000000 0.790244 0.011707 0.070244 0.000000 0.918049 0.000000 0.698537 0.000000 0.301463 0.119024 0.140488 0.000000 0.740488 0.020488 0.243902 0.004878 0.730732 0.000000 0.560000 0.000000 0.440000 0.122927 0.223415 0.038049 0.615610 0.112195 0.094634 0.124878 0.668293 0.055610 0.547317 0.026341 0.370732 0.069268 0.160976 0.000000 0.769756 0.002927 0.239024 0.033171 0.724878 0.020488 0.531707 0.000000 0.447805 0.064390 0.263415 0.094634 0.577561 0.076098 0.168780 0.000000 0.755122 0.101463 0.442927 0.096585 0.359024 0.222439 0.247805 0.160976 0.368780 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTYTTYTTYH MEME-2 regular expression -------------------------------------------------------------------------------- T[CT][TA][TGC][TC][TC]T[CT]T[TC][CT][TC]T[CT]T[TC][CT][TC]T[CT][TCA] -------------------------------------------------------------------------------- Time 231.72 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************