******************************************************************************** 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/AT1G69780_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/AT1G69780_peak_sequences.fasta -dna -oc out/AT1G69780 -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= 7682 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= 1817773 N= 7682 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.377 C 0.123 G 0.123 T 0.377 Background letter frequencies (from file dataset with add-one prior applied): A 0.378 C 0.122 G 0.122 T 0.378 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF THAATTATTDD MEME-1 width = 11 sites = 7652 llr = 48874 E-value = 8.9e-055 ******************************************************************************** -------------------------------------------------------------------------------- Motif THAATTATTDD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 228a:1a::33 pos.-specific C 131:::::::1 probability G 11:::2:::53 matrix T 631:a8:aa33 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 ** ** (9.2 bits) 1.2 ** *** 0.9 ** *** 0.6 ******** 0.3 ********** 0.0 ----------- Multilevel TTAATTATTGA consensus AC AG sequence A TT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif THAATTATTDD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1740952 bayes= 9.862 E= 8.9e-055 -63 -58 -80 68 -78 136 25 -24 100 16 -459 -190 140 -1955 -1955 -891 -950 -587 -1955 140 -254 -376 36 103 140 -587 -1955 -917 -950 -1955 -1955 140 -869 -541 -501 139 -42 -378 190 -58 -29 -16 131 -44 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif THAATTATTDD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 7652 E= 8.9e-055 0.244511 0.081939 0.070439 0.603110 0.219158 0.315212 0.145452 0.320178 0.757710 0.136304 0.005097 0.100889 0.999216 0.000000 0.000000 0.000784 0.000523 0.002091 0.000000 0.997386 0.064820 0.009017 0.156822 0.769341 0.997256 0.002091 0.000000 0.000653 0.000523 0.000000 0.000000 0.999477 0.000915 0.002875 0.003790 0.992420 0.281626 0.008887 0.456613 0.252875 0.308939 0.109775 0.303842 0.277444 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif THAATTATTDD MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TCA]AATTATT[GAT][AGT] -------------------------------------------------------------------------------- Time 125.61 secs. ******************************************************************************** ******************************************************************************** MOTIF CRYYSKTCCMAACYCGKSMCS MEME-2 width = 21 sites = 31 llr = 618 E-value = 2.0e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif CRYYSKTCCMAACYCGKSMCS MEME-2 Description -------------------------------------------------------------------------------- Simplified A :5::22:::59a:::1::511 pos.-specific C 7:454119941:949::5574 probability G :5::553:1:::11:855:14 matrix T 3:64:26::1:::5115:11: bits 3.0 2.7 2.4 ** * * 2.1 ** * ** * Relative 1.8 ** * ** * Entropy 1.5 * ** * ** * (28.8 bits) 1.2 ** * ** ** **** ** 0.9 ***** ** *** ******* 0.6 ********************* 0.3 ********************* 0.0 --------------------- Multilevel CATCGGTCCAAACTCGTGACC consensus TGCTCTG C C GCC G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRYYSKTCCMAACYCGKSMCS MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1664132 bayes= 17.7029 E= 2.0e+001 -1160 247 -1160 -23 54 -1160 188 -1160 -1160 154 -1160 77 -354 216 -192 4 -123 154 188 -354 -96 8 188 -74 -354 -34 125 62 -1160 293 -192 -354 -1160 288 -92 -354 45 154 -192 -196 121 -34 -1160 -354 136 -192 -1160 -1160 -1160 283 8 -1160 -354 166 -92 45 -1160 288 -1160 -196 -255 -1160 278 -196 -1160 -1160 198 45 -1160 188 216 -1160 26 188 -1160 -196 -155 254 -92 -196 -155 178 178 -354 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRYYSKTCCMAACYCGKSMCS MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 31 E= 2.0e+001 0.000000 0.677419 0.000000 0.322581 0.548387 0.000000 0.451613 0.000000 0.000000 0.354839 0.000000 0.645161 0.032258 0.548387 0.032258 0.387097 0.161290 0.354839 0.451613 0.032258 0.193548 0.129032 0.451613 0.225806 0.032258 0.096774 0.290323 0.580645 0.000000 0.935484 0.032258 0.032258 0.000000 0.903226 0.064516 0.032258 0.516129 0.354839 0.032258 0.096774 0.870968 0.096774 0.000000 0.032258 0.967742 0.032258 0.000000 0.000000 0.000000 0.870968 0.129032 0.000000 0.032258 0.387097 0.064516 0.516129 0.000000 0.903226 0.000000 0.096774 0.064516 0.000000 0.838710 0.096774 0.000000 0.000000 0.483871 0.516129 0.000000 0.451613 0.548387 0.000000 0.451613 0.451613 0.000000 0.096774 0.129032 0.709677 0.064516 0.096774 0.129032 0.419355 0.419355 0.032258 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CRYYSKTCCMAACYCGKSMCS MEME-2 regular expression -------------------------------------------------------------------------------- [CT][AG][TC][CT][GC][GT][TG]CC[AC]AAC[TC]CG[TG][GC][AC]C[CG] -------------------------------------------------------------------------------- Time 240.57 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************