******************************************************************************** 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/AT3G24120_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/AT3G24120_peak_sequences.fasta -dna -oc out/AT3G24120 -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= 10622 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= 2205240 N= 10622 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.336 C 0.164 G 0.164 T 0.336 Background letter frequencies (from file dataset with add-one prior applied): A 0.338 C 0.162 G 0.162 T 0.338 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NHRAAGATT MEME-1 width = 9 sites = 10619 llr = 57417 E-value = 8.9e-191 ******************************************************************************** -------------------------------------------------------------------------------- Motif NHRAAGATT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 34469:a:: pos.-specific C 2211::::: probability G 2141:7::: matrix T 322213:aa bits 2.6 2.4 2.1 1.8 Relative 1.6 *** Entropy 1.3 **** (7.8 bits) 1.0 ***** 0.8 ***** 0.5 ***** 0.3 ******* 0.0 --------- Multilevel AAGAAGATT consensus TCAT T sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHRAAGATT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 9 n= 2120264 bayes= 9.82898 E= 8.9e-191 -7 16 12 -8 32 57 -38 -67 13 -159 133 -101 76 -25 -125 -61 144 -452 -643 -219 -2002 -2002 207 -9 157 -2002 -2002 -2002 -2002 -2002 -2002 157 -2002 -2002 -743 157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHRAAGATT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 9 nsites= 10619 E= 8.9e-191 0.321876 0.181373 0.176570 0.320181 0.422639 0.240795 0.124871 0.211696 0.369244 0.054054 0.409172 0.167530 0.573689 0.136171 0.068462 0.221678 0.917224 0.007063 0.001883 0.073830 0.000000 0.000000 0.681797 0.318203 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000942 0.999058 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NHRAAGATT MEME-1 regular expression -------------------------------------------------------------------------------- [AT][ACT][GA][AT]A[GT]ATT -------------------------------------------------------------------------------- Time 73.41 secs. ******************************************************************************** ******************************************************************************** MOTIF TTYTTYTTYTTYTTYTTYTYY MEME-2 width = 21 sites = 1625 llr = 17280 E-value = 4.9e-032 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTYTTYTTYTTYTTYTTYTYY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::::::::1::1:11:::22 pos.-specific C 214225:33214:14214123 probability G 1:11:::::111:1:::221: matrix T 696885a76685875794645 bits 2.6 2.4 2.1 1.8 Relative 1.6 Entropy 1.3 * (15.3 bits) 1.0 * * ** * 0.8 ******** *** ** 0.5 ******** ********* * 0.3 ******************* * 0.0 --------------------- Multilevel TTTTTTTTTTTTTTTTTTTTT consensus C C C CCC C C CGCC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTTYTTYTTYTTYTTYTYY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1992800 bayes= 12.5537 E= 4.9e-032 -174 41 -62 77 -1731 -21 -1731 135 -1731 118 -126 74 -1731 28 -169 116 -1731 17 -1731 128 -293 154 -1731 52 -909 -185 -1731 150 -1731 84 -1731 107 -293 100 -1731 90 -175 34 -70 82 -1731 -68 -103 128 -678 135 -31 42 -158 -804 -170 131 -281 -155 -12 115 -129 133 -1731 43 -191 1 -240 109 -1731 -50 -572 139 -1731 127 3 39 -315 -32 44 86 -95 60 -26 39 -102 90 -1731 65 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTTYTTYTTYTTYTTYTYY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1625 E= 4.9e-032 0.100923 0.216000 0.105846 0.577231 0.000000 0.140308 0.000000 0.859692 0.000000 0.366769 0.067692 0.565538 0.000000 0.196923 0.050462 0.752615 0.000000 0.182769 0.000000 0.817231 0.044308 0.473231 0.000000 0.482462 0.000615 0.044923 0.000000 0.954462 0.000000 0.291692 0.000000 0.708308 0.044308 0.324308 0.000000 0.631385 0.100308 0.205538 0.099692 0.594462 0.000000 0.101538 0.079385 0.819077 0.003077 0.414154 0.131077 0.451692 0.113231 0.000615 0.049846 0.836308 0.048000 0.055385 0.148923 0.747692 0.138462 0.407385 0.000000 0.454154 0.089846 0.163077 0.030769 0.716308 0.000000 0.115077 0.003077 0.881846 0.000000 0.392000 0.166154 0.441846 0.038154 0.129846 0.219692 0.612308 0.174769 0.246769 0.136000 0.442462 0.166769 0.302769 0.000000 0.530462 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTTYTTYTTYTTYTTYTYY MEME-2 regular expression -------------------------------------------------------------------------------- [TC]T[TC]TT[TC]T[TC][TC][TC]T[TC]TT[TC]TT[TC][TG][TC][TC] -------------------------------------------------------------------------------- Time 145.43 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************