******************************************************************************** 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/AT5G60130_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/AT5G60130_peak_sequences.fasta -dna -oc out/AT5G60130 -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= 6444 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= 1230556 N= 6444 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.378 C 0.122 G 0.122 T 0.378 Background letter frequencies (from file dataset with add-one prior applied): A 0.379 C 0.121 G 0.121 T 0.379 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TTTTTYTTTTTTTTTTYTTTYWTTTTBYT MEME-1 width = 29 sites = 2652 llr = 25717 E-value = 2.8e-145 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTTTTYTTTTTTTTTTYTTTYWTTTTBYT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 211::12:1211:::1111223211:111 pos.-specific C 1212241222111122431131111:342 probability G 11::11::1:1:::12::11211:::211 matrix T 67887467667899865666456789446 bits 3.0 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 (14.0 bits) 1.2 0.9 * *** * 0.6 **** * **** ** **** 0.3 ******************* * ******* 0.0 ----------------------------- Multilevel TTTTTCTTTTTTTTTTTTTTTTTTTTTTT consensus CT C C CC ACAA CCC sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTYTTTTTTTTTTYTTTYWTTTTBYT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 1050123 bayes= 10.8824 E= 2.8e-145 -100 16 -77 67 -185 46 -118 83 -215 -23 -237 106 -1802 63 -1802 110 -739 73 10 82 -226 180 -59 14 -106 24 -142 73 -353 104 -134 82 -168 42 28 60 -100 76 -182 59 -160 20 -51 78 -231 -9 -182 103 -1802 -45 -149 120 -404 -20 -387 119 -797 54 -95 100 -217 68 32 59 -197 178 -185 26 -173 106 -674 74 -158 15 20 66 -64 -22 -77 62 -118 113 48 8 -19 -11 -34 28 -79 -80 -60 74 -143 12 -1802 94 -229 -28 -1802 112 -1802 -174 -165 129 -262 120 98 16 -142 157 -85 19 -202 92 -38 62 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTYTTTTTTTTTTYTTTYWTTTTBYT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 2652 E= 2.8e-145 0.190045 0.135747 0.070890 0.603318 0.104827 0.166290 0.053544 0.675339 0.085596 0.103318 0.023379 0.787707 0.000000 0.187783 0.000000 0.812217 0.002262 0.201357 0.129713 0.666667 0.079186 0.421192 0.080694 0.418929 0.181750 0.143288 0.045249 0.629713 0.032805 0.249246 0.047888 0.670060 0.118401 0.161765 0.147059 0.572775 0.190045 0.205128 0.034314 0.570513 0.125189 0.139140 0.084842 0.650830 0.076546 0.113499 0.034314 0.775641 0.000000 0.088612 0.042986 0.868401 0.023002 0.105581 0.008296 0.863122 0.001508 0.176471 0.062594 0.759427 0.084465 0.194193 0.151584 0.569759 0.096531 0.416667 0.033560 0.453243 0.114253 0.253017 0.001131 0.631599 0.126320 0.134615 0.139517 0.599548 0.242459 0.104072 0.070890 0.582579 0.166667 0.264706 0.169306 0.399321 0.332956 0.112368 0.095400 0.459276 0.218703 0.069382 0.079940 0.631976 0.141026 0.131222 0.000000 0.727753 0.077677 0.099548 0.000000 0.822775 0.000000 0.036199 0.038462 0.925339 0.061463 0.278281 0.238311 0.421946 0.141403 0.359351 0.067119 0.432127 0.093514 0.229638 0.092760 0.584087 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTTTTYTTTTTTTTTTYTTTYWTTTTBYT MEME-1 regular expression -------------------------------------------------------------------------------- TTTT[TC][CT]T[TC]T[TC]TTTTTT[TC][TC]T[TA][TC][TA][TA]TTT[TCG][TC][TC] -------------------------------------------------------------------------------- Time 74.69 secs. ******************************************************************************** ******************************************************************************** MOTIF GAYWCKWSSCAMAATCKWATGAGTTASTAAYWTTSAAAACCWTAYTTTAT MEME-2 width = 50 sites = 6 llr = 309 E-value = 1.5e-004 ******************************************************************************** -------------------------------------------------------------------------------- Motif GAYWCKWSSCAMAATCKWATGAGTTASTAAYWTTSAAAACCWTAYTTTAT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :7:7::3:::7577:::3a2:7:::a2:7a:3::277aa::7:a::::7: pos.-specific C ::7:a::33a:3:3:a::::::::::323:7:::333::aa:::5:3:3: probability G a3:::7:77:3:3:::7:::a3a:::5::::::35::::::::::::::: matrix T ::33:37::::2::a:37:8:::aa::8::37a7:::::::3a:5a7a:a bits 3.0 * * * * * * ** 2.7 * * * * * * ** 2.4 * * * * * * ** 2.1 * * *** * * * ** Relative 1.8 * * *** * * * ** Entropy 1.5 * * ** *** *** * * **** ** * **** ** * * * (74.4 bits) 1.2 * * ** *** *** * * ***** ** * * **** **** * * 0.9 *** ** **** ***** * *********** ********* ******** 0.6 ************************************************** 0.3 ************************************************** 0.0 -------------------------------------------------- Multilevel GACACGTGGCAAAATCGTATGAGTTAGTAACTTTGAAAACCATACTTTAT consensus GTT TACC GCGC TA G C C TA GCCC T T C C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAYWCKWSSCAMAATCKWATGAGTTASTAAYWTTSAAAACCWTAYTTTAT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 914799 bayes= 17.6656 E= 1.5e-004 -923 -923 304 -923 81 -923 146 -923 -923 246 -923 -18 81 -923 -923 -18 -923 304 -923 -923 -923 -923 246 -18 -18 -923 -923 81 -923 146 246 -923 -923 146 246 -923 -923 304 -923 -923 81 -923 146 -923 40 146 -923 -118 81 -923 146 -923 81 146 -923 -923 -923 -923 -923 140 -923 304 -923 -923 -923 -923 246 -18 -18 -923 -923 81 140 -923 -923 -923 -118 -923 -923 114 -923 -923 304 -923 81 -923 146 -923 -923 -923 304 -923 -923 -923 -923 140 -923 -923 -923 140 140 -923 -923 -923 -118 146 204 -923 -923 46 -923 114 81 146 -923 -923 140 -923 -923 -923 -923 246 -923 -18 -18 -923 -923 81 -923 -923 -923 140 -923 -923 146 81 -118 146 204 -923 81 146 -923 -923 81 146 -923 -923 140 -923 -923 -923 140 -923 -923 -923 -923 304 -923 -923 -923 304 -923 -923 81 -923 -923 -18 -923 -923 -923 140 140 -923 -923 -923 -923 204 -923 40 -923 -923 -923 140 -923 146 -923 81 -923 -923 -923 140 81 146 -923 -923 -923 -923 -923 140 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAYWCKWSSCAMAATCKWATGAGTTASTAAYWTTSAAAACCWTAYTTTAT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 6 E= 1.5e-004 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.333333 0.000000 0.000000 0.666667 0.000000 0.333333 0.666667 0.000000 0.000000 0.333333 0.666667 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.500000 0.333333 0.000000 0.166667 0.666667 0.000000 0.333333 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.333333 0.000000 0.000000 0.666667 1.000000 0.000000 0.000000 0.000000 0.166667 0.000000 0.000000 0.833333 0.000000 0.000000 1.000000 0.000000 0.666667 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.166667 0.333333 0.500000 0.000000 0.000000 0.166667 0.000000 0.833333 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.666667 0.000000 0.333333 0.333333 0.000000 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.333333 0.666667 0.166667 0.333333 0.500000 0.000000 0.666667 0.333333 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.000000 0.000000 0.333333 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.000000 0.000000 1.000000 0.000000 0.333333 0.000000 0.666667 0.000000 0.000000 0.000000 1.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GAYWCKWSSCAMAATCKWATGAGTTASTAAYWTTSAAAACCWTAYTTTAT MEME-2 regular expression -------------------------------------------------------------------------------- G[AG][CT][AT]C[GT][TA][GC][GC]C[AG][AC][AG][AC]TC[GT][TA]ATG[AG]GTTA[GC]T[AC]A[CT][TA]T[TG][GC][AC][AC]AACC[AT]TA[CT]T[TC]T[AC]T -------------------------------------------------------------------------------- Time 146.92 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************