******************************************************************************** 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/AT1G52880_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/AT1G52880_peak_sequences.fasta -dna -oc out/AT1G52880 -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= 1340 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= 178534 N= 1340 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 0.319 C 0.181 G 0.181 T 0.319 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF ACACGTAACYW MEME-1 width = 11 sites = 1336 llr = 9480 E-value = 2.7e-459 ******************************************************************************** -------------------------------------------------------------------------------- Motif ACACGTAACYW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 61a::178112 pos.-specific C 15:a:23:541 probability G 11::a2::112 matrix T 23:::512354 bits 2.5 ** 2.2 ** 2.0 ** 1.7 *** Relative 1.5 *** Entropy 1.2 *** (10.2 bits) 1.0 *** * 0.7 *** ** 0.5 **** *** 0.2 ********** 0.0 ----------- Multilevel ACACGTAACTT consensus TT CC TCA sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACGTAACYW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 165134 bayes= 7.55082 E= 2.7e-459 92 -169 -47 -59 -262 157 -37 -25 165 -1703 -1703 -1703 -593 246 -1703 -1703 -1703 -511 246 -1703 -243 45 -18 74 105 61 -1703 -232 134 -634 -534 -78 -157 159 -123 -24 -179 96 -93 53 -46 -68 22 48 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACGTAACYW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1336 E= 2.7e-459 0.601796 0.056138 0.130988 0.211078 0.051647 0.540419 0.139970 0.267964 1.000000 0.000000 0.000000 0.000000 0.005240 0.994760 0.000000 0.000000 0.000000 0.005240 0.994760 0.000000 0.059132 0.247754 0.160180 0.532934 0.660180 0.276198 0.000000 0.063623 0.807635 0.002246 0.004491 0.185629 0.107036 0.546407 0.077096 0.269461 0.092066 0.351796 0.095060 0.461078 0.231287 0.113024 0.211078 0.444611 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ACACGTAACYW MEME-1 regular expression -------------------------------------------------------------------------------- [AT][CT]ACG[TC][AC]A[CT][TC][TAG] -------------------------------------------------------------------------------- Time 132.80 secs. ******************************************************************************** ******************************************************************************** MOTIF YTYTCTYYYTCTYYTTYTYY MEME-2 width = 20 sites = 203 llr = 2131 E-value = 1.0e-040 ******************************************************************************** -------------------------------------------------------------------------------- Motif YTYTCTYYYTCTYYTTYTYY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1:::::1:1::1::1::111 pos.-specific C 325:71433:71343:5134 probability G 1::111::1:::1:122211 matrix T 58593866593865583664 bits 2.5 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 * ** (15.1 bits) 1.0 * *** ** * 0.7 ******* ***** ** 0.5 ************* ** * 0.2 ******************** 0.0 -------------------- Multilevel TTTTCTTTTTCTTTTTCTTC consensus CCC T CCC T CCC T CT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYTCTYYYTCTYYTTYTYY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 153074 bayes= 11.4846 E= 1.0e-040 -243 84 -50 61 -1431 38 -420 124 -443 138 -362 64 -301 -1431 -174 151 -1431 184 -95 -31 -1431 -130 -112 140 -256 105 -1431 84 -269 91 -1431 94 -231 82 -120 75 -1431 -262 -203 154 -1431 192 -288 -13 -231 -103 -239 135 -1431 91 -174 93 -1431 122 -239 77 -149 53 -120 78 -369 -420 -16 133 -1431 138 -3 13 -162 -40 -12 89 -243 73 -130 83 -149 126 -95 17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYTCTYYYTCTYYTTYTYY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 203 E= 1.0e-040 0.059113 0.325123 0.128079 0.487685 0.000000 0.236453 0.009852 0.753695 0.014778 0.472906 0.014778 0.497537 0.039409 0.000000 0.054187 0.906404 0.000000 0.650246 0.093596 0.256158 0.000000 0.073892 0.083744 0.842365 0.054187 0.374384 0.000000 0.571429 0.049261 0.339901 0.000000 0.610837 0.064039 0.320197 0.078818 0.536946 0.000000 0.029557 0.044335 0.926108 0.000000 0.684729 0.024631 0.290640 0.064039 0.088670 0.034483 0.812808 0.000000 0.339901 0.054187 0.605911 0.000000 0.423645 0.034483 0.541872 0.113300 0.261084 0.078818 0.546798 0.024631 0.009852 0.162562 0.802956 0.000000 0.472906 0.177340 0.349754 0.103448 0.137931 0.167488 0.591133 0.059113 0.300493 0.073892 0.566502 0.113300 0.433498 0.093596 0.359606 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YTYTCTYYYTCTYYTTYTYY MEME-2 regular expression -------------------------------------------------------------------------------- [TC][TC][TC]T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[CT]T[TC][CT] -------------------------------------------------------------------------------- Time 239.30 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************