******************************************************************************** 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/AT5G05790_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/AT5G05790_peak_sequences.fasta -dna -oc out/AT5G05790 -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= 4825 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= 949192 N= 4825 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.338 C 0.162 G 0.162 T 0.338 Background letter frequencies (from file dataset with add-one prior applied): A 0.34 C 0.16 G 0.16 T 0.34 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HWWWYCTTATCYWNW MEME-1 width = 15 sites = 4802 llr = 33732 E-value = 1.1e-218 ******************************************************************************** -------------------------------------------------------------------------------- Motif HWWWYCTTATCYWNW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3346:2::a::2335 pos.-specific C 221146:1::a313: probability G 112111:1::::12: matrix T 443351a8:a:5534 bits 2.6 * 2.4 * 2.1 * 1.9 * Relative 1.6 *** Entropy 1.3 * *** (10.1 bits) 1.1 * *** 0.8 ****** 0.5 ******* 0.3 ********* * 0.0 --------------- Multilevel TTAATCTTATCTTTA consensus AATTCA CACT sequence C A G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HWWWYCTTATCYWNW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 881642 bayes= 9.56156 E= 1.1e-218 3 42 -88 5 -28 23 -41 27 37 -31 6 -36 70 -136 -109 -14 -279 126 -152 59 -64 183 -48 -178 -374 -409 -1887 151 -628 -67 -160 131 156 -1887 -1887 -1887 -1887 -1887 -958 156 -1887 264 -1887 -1887 -89 90 -184 48 -15 -15 -72 41 -38 71 36 -32 58 -168 -234 27 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HWWWYCTTATCYWNW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4802 E= 1.1e-218 0.348188 0.213661 0.086839 0.351312 0.280508 0.188047 0.120367 0.411079 0.439192 0.128905 0.166597 0.265306 0.553519 0.062266 0.075177 0.309038 0.049146 0.383382 0.055602 0.511870 0.218659 0.568305 0.114327 0.098709 0.025406 0.009371 0.000000 0.965223 0.004373 0.100791 0.052895 0.841941 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000208 0.999792 0.000000 1.000000 0.000000 0.000000 0.182840 0.299250 0.044773 0.473136 0.306955 0.144107 0.096835 0.452103 0.260516 0.260933 0.205956 0.272595 0.509579 0.049771 0.031653 0.408996 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HWWWYCTTATCYWNW MEME-1 regular expression -------------------------------------------------------------------------------- [TAC][TA][AT][AT][TC][CA]TTATC[TC][TA][TCAG][AT] -------------------------------------------------------------------------------- Time 73.57 secs. ******************************************************************************** ******************************************************************************** MOTIF TCATCWTCWTCWTCWTCHTCHTCWYCWTC MEME-2 width = 29 sites = 437 llr = 5633 E-value = 2.2e-036 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCATCWTCWTCWTCWTCHTCHTCWYCWTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 116115::41:41:41:311411521511 pos.-specific C 27227119128118216227217136127 probability G 11:11:1:1:111:::1:1:11:1111:1 matrix T 61261581471472492462361351381 bits 2.6 2.4 2.1 * 1.9 * Relative 1.6 * * Entropy 1.3 * * * (18.6 bits) 1.1 * ** * * * * * * 0.8 * * ** * * ** * * * ** 0.5 * * ** ** ** ** * ** * ** 0.3 ******** ** ** ***** ** ** ** 0.0 ----------------------------- Multilevel TCATCTTCTTCTTCTTCTTCATCATCATC consensus T A A A A TACTT TC T sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATCWTCWTCWTCWTCHTCHTCWYCWTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 814092 bayes= 12.9879 E= 2.2e-036 -160 32 -137 88 -201 213 -51 -172 74 19 -613 -47 -128 0 -117 89 -166 203 -67 -131 41 -122 -613 49 -1542 -51 -167 130 -1542 251 -1542 -193 19 -29 -117 27 -169 23 -1542 106 -721 223 -48 -138 17 -108 -77 40 -263 -17 -88 107 -297 227 -1542 -88 15 -8 -196 34 -269 -74 -1542 132 -321 201 -67 -65 -14 63 -243 28 -131 40 -108 76 -251 205 -181 -56 17 47 -67 -20 -241 -13 -17 93 -157 214 -213 -124 59 -67 -113 -11 -117 67 -84 57 -124 195 -35 -163 51 -11 -88 -27 -236 -6 -1542 120 -257 215 -46 -157 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATCWTCWTCWTCWTCHTCHTCWYCWTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 437 E= 2.2e-036 0.112128 0.199085 0.061785 0.627002 0.084668 0.700229 0.112128 0.102975 0.569794 0.183066 0.002288 0.244851 0.139588 0.160183 0.070938 0.629291 0.107551 0.654462 0.100686 0.137300 0.453089 0.068650 0.002288 0.475973 0.000000 0.112128 0.050343 0.837529 0.000000 0.910755 0.000000 0.089245 0.389016 0.130435 0.070938 0.409611 0.105263 0.187643 0.000000 0.707094 0.002288 0.752860 0.114416 0.130435 0.382151 0.075515 0.093822 0.448513 0.054920 0.141876 0.086957 0.716247 0.043478 0.771167 0.000000 0.185355 0.377574 0.151030 0.041190 0.430206 0.052632 0.096110 0.000000 0.851259 0.036613 0.645309 0.100686 0.217391 0.308924 0.247140 0.029748 0.414188 0.137300 0.210526 0.075515 0.576659 0.059497 0.663616 0.045767 0.231121 0.382151 0.221968 0.100686 0.295195 0.064073 0.146453 0.141876 0.647597 0.114416 0.704805 0.036613 0.144165 0.510297 0.100686 0.073227 0.315789 0.151030 0.254005 0.089245 0.505721 0.144165 0.620137 0.125858 0.109840 0.482838 0.148741 0.086957 0.281465 0.066362 0.153318 0.000000 0.780320 0.057208 0.711670 0.116705 0.114416 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCATCWTCWTCWTCWTCHTCHTCWYCWTC MEME-2 regular expression -------------------------------------------------------------------------------- TC[AT]TC[TA]TC[TA]TC[TA]TC[TA]T[CT][TAC][TC][CT][ATC]TC[AT][TC]C[AT]TC -------------------------------------------------------------------------------- Time 137.57 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************