******************************************************************************** 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/AT3G18990_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/AT3G18990_peak_sequences.fasta -dna -oc out/AT3G18990 -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= 7073 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= 1574026 N= 7073 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.379 C 0.121 G 0.121 T 0.379 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 WTTTTTTTTTTTTTTTTTTTK MEME-1 width = 21 sites = 6482 llr = 67724 E-value = 5.0e-679 ******************************************************************************** -------------------------------------------------------------------------------- Motif WTTTTTTTTTTTTTTTTTTTK MEME-1 Description -------------------------------------------------------------------------------- Simplified A 322212:1:11::::1::::2 pos.-specific C 1121111:1:::::::::1:1 probability G 11111:1:1:::::::::123 matrix T 565668898999a999aa984 bits 3.1 2.7 2.4 2.1 Relative 1.8 Entropy 1.5 (15.1 bits) 1.2 * ** 0.9 ******** *** 0.6 *************** 0.3 ******************** 0.0 --------------------- Multilevel TTTTTTTTTTTTTTTTTTTTT consensus AA A GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTTTTTTTTTTTTTTTTK MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1432566 bayes= 9.99879 E= 5.0e-679 -59 26 -5 36 -85 -100 2 68 -118 49 -3 52 -91 -87 -53 77 -137 -67 25 74 -102 -126 -861 101 -322 -27 -52 103 -154 -961 -629 119 -1126 -70 -62 116 -256 -1931 -680 130 -238 -241 -861 125 -571 -208 -182 129 -328 -1931 -1931 134 -398 -186 -383 130 -496 -133 -171 125 -263 -204 -142 119 -1931 -1931 -195 135 -1931 -961 -433 139 -1931 -109 -59 119 -369 -295 74 99 -112 -6 146 0 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTTTTTTTTTTTTTTTTK MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 6482 E= 5.0e-679 0.252700 0.144400 0.116322 0.486578 0.211200 0.060475 0.122493 0.605832 0.167232 0.169546 0.117711 0.545511 0.201790 0.065875 0.083770 0.648565 0.146560 0.075902 0.143629 0.633909 0.186979 0.050447 0.000309 0.762265 0.040728 0.100278 0.084233 0.774761 0.130515 0.000154 0.001543 0.867788 0.000154 0.074205 0.078217 0.847424 0.064178 0.000000 0.001080 0.934742 0.072663 0.022678 0.000309 0.904351 0.007251 0.028541 0.034094 0.930114 0.039031 0.000000 0.000000 0.960969 0.024067 0.033323 0.008485 0.934125 0.012188 0.047979 0.036871 0.902962 0.061247 0.029312 0.045048 0.864394 0.000000 0.000000 0.031317 0.968683 0.000000 0.000154 0.006017 0.993829 0.000000 0.056618 0.080376 0.863005 0.029312 0.015582 0.201635 0.753471 0.174329 0.115396 0.331996 0.378278 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTTTTTTTTTTTTTTTTTTTK MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TA]T[TA]TTTTTTTTTTTTTTT[TG][TG] -------------------------------------------------------------------------------- Time 67.02 secs. ******************************************************************************** ******************************************************************************** MOTIF AWYAWGTAAYKTSMWRCYRAACYCKTCCCGCCAAWYYYKTSSCGHMAAAA MEME-2 width = 50 sites = 20 llr = 849 E-value = 3.1e-031 ******************************************************************************** -------------------------------------------------------------------------------- Motif AWYAWGTAAYKTSMWRCYRAACYCKTCCCGCCAAWYYYKTSSCGHMAAAA MEME-2 Description -------------------------------------------------------------------------------- Simplified A a4:96::99121:4441:7982:11::::1:1a95::111::1134aa99 pos.-specific C 114:::111611661:a6::1857:2899:a811256512668146::11 probability G :::11a:11:4341:6::41112:6::119::::1::24:4417::::11 matrix T :671419::4461:51:5:11:43492111:1:1364468:11241:::: bits 3.1 * 2.7 * * * 2.4 * * ** 2.1 * * ***** * Relative 1.8 * * * * ****** ** Entropy 1.5 * * * * ****** * *** ** (61.3 bits) 1.2 * ** * ** ** * * ******* ** **** ** 0.9 * ** ***** ** ***** ************* ** **** ***** 0.6 * ** ********* ******************* ********* ***** 0.3 ********************************** *************** 0.0 -------------------------------------------------- Multilevel ATTAAGTAACGTCCTGCCAAACCCGTCCCGCCAAATCCTTCCCGCCAAAA consensus AC T TTGGAAA TG TTT T TCTTGCGG TTA sequence C A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWYAWGTAAYKTSMWRCYRAACYCKTCCCGCCAAWYYYKTSSCGHMAAAA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 50 n= 1227449 bayes= 16.1568 E= 3.1e-031 132 -127 -1097 -1097 8 -127 -1097 54 -1097 154 -1097 78 116 -1097 -27 -292 54 -1097 -127 8 -1097 -1097 298 -292 -1097 -27 -1097 125 125 -127 -127 -1097 125 -127 -127 -1097 -292 219 -1097 8 -134 -127 173 8 -292 -127 131 66 -1097 231 154 -292 8 219 -127 -1097 8 -27 -1097 40 -12 -1097 219 -192 -292 298 -1097 -1097 -1097 219 -1097 25 78 -1097 154 -1097 125 -1097 -127 -292 108 -27 -127 -292 -134 264 -27 -1097 -1097 205 31 -12 -292 243 -1097 -34 -192 -1097 219 -12 -1097 31 -1097 116 -1097 273 -1097 -92 -1097 282 -27 -292 -1097 282 -127 -192 -292 -1097 290 -292 -1097 305 -1097 -1097 -192 273 -1097 -192 132 -127 -1097 -1097 116 -27 -1097 -292 40 73 -127 -60 -1097 190 -1097 54 -1097 231 -1097 8 -292 190 31 -12 -292 -127 154 54 -292 73 -1097 98 -1097 231 173 -1097 -1097 231 154 -292 -192 264 -127 -192 -292 -27 243 -92 -34 154 -1097 -12 -12 219 -1097 -192 140 -1097 -1097 -1097 140 -1097 -1097 -1097 125 -127 -127 -1097 116 -127 -27 -1097 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWYAWGTAAYKTSMWRCYRAACYCKTCCCGCCAAWYYYKTSSCGHMAAAA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 50 nsites= 20 E= 3.1e-031 0.950000 0.050000 0.000000 0.000000 0.400000 0.050000 0.000000 0.550000 0.000000 0.350000 0.000000 0.650000 0.850000 0.000000 0.100000 0.050000 0.550000 0.000000 0.050000 0.400000 0.000000 0.000000 0.950000 0.050000 0.000000 0.100000 0.000000 0.900000 0.900000 0.050000 0.050000 0.000000 0.900000 0.050000 0.050000 0.000000 0.050000 0.550000 0.000000 0.400000 0.150000 0.050000 0.400000 0.400000 0.050000 0.050000 0.300000 0.600000 0.000000 0.600000 0.350000 0.050000 0.400000 0.550000 0.050000 0.000000 0.400000 0.100000 0.000000 0.500000 0.350000 0.000000 0.550000 0.100000 0.050000 0.950000 0.000000 0.000000 0.000000 0.550000 0.000000 0.450000 0.650000 0.000000 0.350000 0.000000 0.900000 0.000000 0.050000 0.050000 0.800000 0.100000 0.050000 0.050000 0.150000 0.750000 0.100000 0.000000 0.000000 0.500000 0.150000 0.350000 0.050000 0.650000 0.000000 0.300000 0.100000 0.000000 0.550000 0.350000 0.000000 0.150000 0.000000 0.850000 0.000000 0.800000 0.000000 0.200000 0.000000 0.850000 0.100000 0.050000 0.000000 0.850000 0.050000 0.100000 0.050000 0.000000 0.900000 0.050000 0.000000 1.000000 0.000000 0.000000 0.100000 0.800000 0.000000 0.100000 0.950000 0.050000 0.000000 0.000000 0.850000 0.100000 0.000000 0.050000 0.500000 0.200000 0.050000 0.250000 0.000000 0.450000 0.000000 0.550000 0.000000 0.600000 0.000000 0.400000 0.050000 0.450000 0.150000 0.350000 0.050000 0.050000 0.350000 0.550000 0.050000 0.200000 0.000000 0.750000 0.000000 0.600000 0.400000 0.000000 0.000000 0.600000 0.350000 0.050000 0.100000 0.750000 0.050000 0.100000 0.050000 0.100000 0.650000 0.200000 0.300000 0.350000 0.000000 0.350000 0.350000 0.550000 0.000000 0.100000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.900000 0.050000 0.050000 0.000000 0.850000 0.050000 0.100000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AWYAWGTAAYKTSMWRCYRAACYCKTCCCGCCAAWYYYKTSSCGHMAAAA MEME-2 regular expression -------------------------------------------------------------------------------- A[TA][TC]A[AT]GTAA[CT][GT][TG][CG][CA][TA][GA]C[CT][AG]AAC[CT][CT][GT]T[CT]CCGCCAA[ATC][TC][CT][CT][TG][TC][CG][CG]C[GT][CTA][CA]AAAA -------------------------------------------------------------------------------- Time 133.01 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************