******************************************************************************** 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/AT1G06280_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/AT1G06280_peak_sequences.fasta -dna -oc out/AT1G06280 -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= 4247 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= 645440 N= 4247 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.289 C 0.211 G 0.211 T 0.289 Background letter frequencies (from file dataset with add-one prior applied): A 0.291 C 0.209 G 0.209 T 0.291 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HTCCGAWTTTTTCGG MEME-1 width = 15 sites = 4226 llr = 33288 E-value = 7.6e-627 ******************************************************************************** -------------------------------------------------------------------------------- Motif HTCCGAWTTTTTCGG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2211:63311211:1 pos.-specific C 3269:12112228:2 probability G 122:8211::1::96 matrix T 451:22469757111 bits 2.3 2.0 * 1.8 * * 1.6 * * Relative 1.4 ** ** Entropy 1.1 ** * ** (11.4 bits) 0.9 ** * ** 0.7 *** ** **** 0.5 *** *** **** 0.2 **** ******** 0.0 --------------- Multilevel TTCCGATTTTTTCGG consensus C G AA C sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTCCGAWTTTTTCGG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 585982 bayes= 8.86416 E= 7.6e-627 -54 66 -87 29 -68 -29 -21 68 -198 157 4 -172 -246 218 -1869 -1869 -269 -1869 193 -87 103 -151 -31 -82 3 -38 -65 49 -11 -184 -173 107 -183 -203 -498 157 -224 -30 -298 135 -87 -31 -57 87 -188 -27 -218 127 -129 198 -527 -253 -1869 -1869 217 -236 -195 17 151 -166 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTCCGAWTTTTTCGG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4226 E= 7.6e-627 0.199716 0.330573 0.114766 0.354946 0.181496 0.171320 0.181496 0.465689 0.073829 0.623521 0.214624 0.088027 0.052769 0.947231 0.000000 0.000000 0.044960 0.000000 0.796025 0.159016 0.592286 0.073355 0.169191 0.165168 0.297208 0.161145 0.132986 0.408661 0.269285 0.058448 0.062944 0.609323 0.081637 0.051349 0.006626 0.860388 0.061524 0.169427 0.026503 0.742546 0.158779 0.168717 0.141268 0.531235 0.078798 0.174160 0.046143 0.700899 0.118788 0.825603 0.005442 0.050166 0.000000 0.000000 0.943445 0.056555 0.075248 0.235211 0.597492 0.092049 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTCCGAWTTTTTCGG MEME-1 regular expression -------------------------------------------------------------------------------- [TC]T[CG]CGA[TA][TA]TTTTCG[GC] -------------------------------------------------------------------------------- Time 129.18 secs. ******************************************************************************** ******************************************************************************** MOTIF RAAGAAGRAGAARRAGARRRA MEME-2 width = 21 sites = 620 llr = 6906 E-value = 1.7e-055 ******************************************************************************** -------------------------------------------------------------------------------- Motif RAAGAAGRAGAARRAGARRRA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 476375358286459294646 pos.-specific C :111:1::1::1:::::111: probability G 63262264182255:814343 matrix T ::1:11:::::1::1::::11 bits 2.3 2.0 1.8 1.6 Relative 1.4 * ** Entropy 1.1 * *** (16.1 bits) 0.9 * ***** **** 0.7 ** ** ***** ***** * * 0.5 ** ** ***** ********* 0.2 ********************* 0.0 --------------------- Multilevel GAAGAAGAAGAAGGAGAGAGA consensus AG AGGAG GGAA AGAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAGAAGRAGAARRAGARRRA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 560500 bayes= 11.871 E= 1.7e-055 30 -470 149 -269 119 -193 28 -341 103 -81 -39 -117 -14 -156 161 -341 126 -1592 4 -169 79 -64 7 -102 5 -221 157 -325 87 -1592 104 -297 141 -116 -89 -379 -61 -1592 192 -403 137 -1592 15 -403 101 -132 -2 -123 43 -221 133 -297 67 -221 124 -1592 159 -232 -1592 -177 -79 -1592 197 -491 160 -702 -87 -1592 40 -54 107 -310 103 -143 62 -517 53 -147 105 -200 115 -1592 30 -161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAGAAGRAGAARRAGARRRA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 620 E= 1.7e-055 0.358065 0.008065 0.588710 0.045161 0.662903 0.054839 0.254839 0.027419 0.591935 0.119355 0.159677 0.129032 0.264516 0.070968 0.637097 0.027419 0.695161 0.000000 0.214516 0.090323 0.503226 0.133871 0.219355 0.143548 0.301613 0.045161 0.622581 0.030645 0.532258 0.000000 0.430645 0.037097 0.772581 0.093548 0.112903 0.020968 0.190323 0.000000 0.791935 0.017742 0.750000 0.000000 0.232258 0.017742 0.585484 0.083871 0.206452 0.124194 0.391935 0.045161 0.525806 0.037097 0.461290 0.045161 0.493548 0.000000 0.872581 0.041935 0.000000 0.085484 0.167742 0.000000 0.822581 0.009677 0.883871 0.001613 0.114516 0.000000 0.382258 0.143548 0.440323 0.033871 0.591935 0.077419 0.322581 0.008065 0.419355 0.075806 0.432258 0.072581 0.646774 0.000000 0.258065 0.095161 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RAAGAAGRAGAARRAGARRRA MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG]A[GA][AG][AG][GA][AG]AG[AG][AG][GA][GA]AGA[GA][AG][GA][AG] -------------------------------------------------------------------------------- Time 234.80 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************