******************************************************************************** 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/AT2G35530_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/AT2G35530_peak_sequences.fasta -dna -oc out/AT2G35530 -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= 4063 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= 904119 N= 4063 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.3 C 0.2 G 0.2 T 0.3 Background letter frequencies (from file dataset with add-one prior applied): A 0.301 C 0.199 G 0.199 T 0.301 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGCCACGTSDNMWHH MEME-1 width = 15 sites = 3966 llr = 37235 E-value = 1.2e-592 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCCACGTSDNMWHH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2:3:a:1:1423433 pos.-specific C 2:7a:9::4:35223 probability G 18::::9:5331121 matrix T 52:::::a:322333 bits 2.3 * 2.1 * 1.9 * ** 1.6 ***** Relative 1.4 ***** Entropy 1.2 ******* (13.5 bits) 0.9 ******* 0.7 ******** 0.5 ******** 0.2 ********** * 0.0 --------------- Multilevel TGCCACGTGACCATT consensus CTA CTGATAA sequence GT CC A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCACGTSDNMWHH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 847237 bayes= 9.96918 E= 1.2e-592 -92 6 -102 83 -362 -545 193 -49 9 177 -1860 -742 -864 233 -1860 -1860 171 -1860 -1860 -480 -590 225 -304 -362 -237 -296 220 -864 -742 -1860 -1860 173 -136 89 133 -420 39 -395 40 13 -46 48 38 -29 -21 124 -145 -59 34 -16 -41 -5 1 2 -35 18 -6 48 -86 11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCACGTSDNMWHH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 3966 E= 1.2e-592 0.159607 0.207010 0.098084 0.535300 0.024458 0.004539 0.756934 0.214070 0.319970 0.678265 0.000000 0.001765 0.000756 0.999244 0.000000 0.000000 0.989158 0.000000 0.000000 0.010842 0.005043 0.946293 0.024206 0.024458 0.058245 0.025466 0.915532 0.000756 0.001765 0.000000 0.000000 0.998235 0.117247 0.368381 0.497983 0.016389 0.395108 0.012859 0.262733 0.329299 0.218356 0.276601 0.259203 0.245840 0.259960 0.467474 0.072869 0.199697 0.382753 0.177761 0.149269 0.290217 0.302824 0.200706 0.155825 0.340645 0.289460 0.276853 0.109430 0.324256 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCACGTSDNMWHH MEME-1 regular expression -------------------------------------------------------------------------------- [TC][GT][CA]CACGT[GC][ATG][CGTA][CA][AT][TAC][TAC] -------------------------------------------------------------------------------- Time 118.98 secs. ******************************************************************************** ******************************************************************************** MOTIF AARAARAARAARAARAARARA MEME-2 width = 21 sites = 980 llr = 10153 E-value = 9.4e-059 ******************************************************************************** -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARARA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 784977686985876765845 pos.-specific C :111::11::1:11:121:11 probability G 315:23214:141131:4:32 matrix T 11:::::1:::1:11:2:222 bits 2.3 2.1 1.9 1.6 Relative 1.4 * * Entropy 1.2 * * * (14.9 bits) 0.9 * * ** * * 0.7 ****** ****** * * 0.5 ******************* 0.2 ********************* 0.0 --------------------- Multilevel AAGAAAAAAAAAAAAAAAAAA consensus G A GG G G G G GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARARA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 822859 bayes= 11.9439 E= 9.4e-059 112 -302 45 -256 133 -95 -121 -253 46 -85 126 -1658 163 -177 -602 -562 129 -290 0 -296 111 -1658 81 -1658 105 -95 28 -316 132 -177 -77 -206 87 -402 114 -1658 165 -402 -215 -1658 134 -85 -82 -462 69 -1658 105 -153 134 -118 -41 -1658 112 -51 -76 -181 97 -285 62 -196 124 -77 -43 -356 110 -37 -328 -73 80 -148 90 -325 144 -1658 -1658 -75 54 -113 59 -80 86 -196 -19 -40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARARA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 980 E= 9.4e-059 0.653061 0.024490 0.271429 0.051020 0.759184 0.103061 0.085714 0.052041 0.415306 0.110204 0.474490 0.000000 0.932653 0.058163 0.003061 0.006122 0.735714 0.026531 0.198980 0.038776 0.651020 0.000000 0.348980 0.000000 0.622449 0.103061 0.240816 0.033673 0.753061 0.058163 0.116327 0.072449 0.551020 0.012245 0.436735 0.000000 0.942857 0.012245 0.044898 0.000000 0.765306 0.110204 0.112245 0.012245 0.484694 0.000000 0.411224 0.104082 0.763265 0.087755 0.148980 0.000000 0.657143 0.139796 0.117347 0.085714 0.588776 0.027551 0.306122 0.077551 0.711224 0.116327 0.146939 0.025510 0.643878 0.154082 0.020408 0.181633 0.526531 0.071429 0.370408 0.031633 0.820408 0.000000 0.000000 0.179592 0.437755 0.090816 0.297959 0.173469 0.545918 0.051020 0.174490 0.228571 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AARAARAARAARAARAARARA MEME-2 regular expression -------------------------------------------------------------------------------- [AG]A[GA]AA[AG][AG]A[AG]AA[AG]AA[AG]AA[AG]A[AG][AT] -------------------------------------------------------------------------------- Time 224.90 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************