******************************************************************************** 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/AT4G18450_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/AT4G18450_peak_sequences.fasta -dna -oc out/AT4G18450 -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= 2883 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= 671469 N= 2883 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.251 C 0.249 G 0.249 T 0.251 Background letter frequencies (from file dataset with add-one prior applied): A 0.252 C 0.248 G 0.248 T 0.252 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YHNYYDYCDCCGCCGCCRYHD MEME-1 width = 21 sites = 2867 llr = 27805 E-value = 8.2e-665 ******************************************************************************** -------------------------------------------------------------------------------- Motif YHNYYDYCDCCGCCGCCRYHD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 222223222121:::::3133 pos.-specific C 44245155168:aa:8a:431 probability G 2132131:31:9::a::6113 matrix T 3233333242:1:::1:1433 bits 2.0 * 1.8 *** * 1.6 *** * 1.4 **** * Relative 1.2 ******* Entropy 1.0 ******* (14.0 bits) 0.8 ******* 0.6 ******** 0.4 * ********* 0.2 ** ** ************* * 0.0 --------------------- Multilevel CCGCCGCCTCCGCCGCCGCTA consensus TTTTTTTTGT ATCG sequence AA A A AT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHNYYDYCDCCGCCGCCRYHD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 613809 bayes= 9.93917 E= 8.2e-665 -45 71 -66 0 -22 76 -94 -10 -4 -57 36 10 -72 78 -62 3 -50 91 -125 0 7 -90 31 23 -74 89 -129 19 -34 108 -259 -10 -10 -151 37 50 -185 116 -81 -11 -70 172 -380 -510 -195 -1813 182 -217 -503 198 -589 -464 -749 201 -1813 -1813 -327 -1813 196 -579 -1813 175 -253 -103 -337 197 -947 -1813 26 -947 118 -87 -85 60 -111 56 7 27 -94 29 36 -153 35 12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHNYYDYCDCCGCCGCCRYHD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2867 E= 8.2e-665 0.184165 0.407743 0.156958 0.251134 0.216254 0.419254 0.129055 0.235438 0.245553 0.167422 0.318103 0.268922 0.153122 0.427973 0.161842 0.257063 0.177886 0.465644 0.104639 0.251831 0.263341 0.132892 0.308336 0.295431 0.151029 0.459365 0.101849 0.287757 0.198814 0.525985 0.041158 0.234043 0.234391 0.087199 0.321939 0.356470 0.069759 0.555284 0.141263 0.233694 0.155215 0.819672 0.017789 0.007325 0.065225 0.000000 0.878968 0.055807 0.007674 0.978026 0.004186 0.010115 0.001395 0.998605 0.000000 0.000000 0.026160 0.000000 0.969306 0.004534 0.000000 0.833624 0.042902 0.123474 0.024416 0.975235 0.000349 0.000000 0.300314 0.000349 0.561911 0.137426 0.139170 0.376352 0.114754 0.369724 0.264737 0.299268 0.129055 0.306941 0.322986 0.086153 0.317405 0.273457 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHNYYDYCDCCGCCGCCRYHD MEME-1 regular expression -------------------------------------------------------------------------------- [CT][CTA][GTA][CT][CT][GTA][CT][CT][TGA][CT]CGCCGCC[GA][CT][TCA][AGT] -------------------------------------------------------------------------------- Time 68.90 secs. ******************************************************************************** ******************************************************************************** MOTIF GRAGRAGAARRAGAARRAGAR MEME-2 width = 21 sites = 1488 llr = 14237 E-value = 6.2e-137 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRAGRAGAARRAGAARRAGAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 255247265347165357284 pos.-specific C :12:11:12:11:11:11::1 probability G 64175183265:932641823 matrix T 1:21:1::1112::2::1::2 bits 2.0 1.8 1.6 1.4 * Relative 1.2 * ** Entropy 1.0 * * ** (13.8 bits) 0.8 * ** * ** 0.6 * * *** ***** ***** 0.4 ******** ***** ***** 0.2 ********************* 0.0 --------------------- Multilevel GAAGGAGAAGGAGAAGAAGAA consensus AG A GCAA GGAG A G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGRAGAARRAGAARRAGAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 613809 bayes= 10.7804 E= 6.2e-137 -13 -258 135 -141 106 -177 51 -242 112 -38 -144 -55 -55 -253 147 -137 69 -124 88 -299 140 -106 -174 -82 -44 -283 162 -402 129 -210 22 -274 88 -15 -31 -117 37 -401 127 -209 54 -212 107 -223 137 -103 -251 -47 -96 -1718 180 -496 134 -228 22 -334 98 -104 -11 -71 43 -462 128 -246 89 -146 81 -523 149 -160 -78 -192 -31 -1718 168 -1718 171 -694 -51 -854 77 -135 15 -35 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGRAGAARRAGAARRAGAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1488 E= 6.2e-137 0.229167 0.041667 0.634409 0.094758 0.526210 0.072581 0.354167 0.047043 0.545699 0.191532 0.091398 0.171371 0.172043 0.043011 0.687500 0.097446 0.405242 0.105511 0.457661 0.031586 0.663978 0.118952 0.074597 0.142473 0.185484 0.034946 0.764113 0.015457 0.614247 0.057796 0.290323 0.037634 0.463038 0.224462 0.200941 0.111559 0.325941 0.015457 0.599462 0.059140 0.366263 0.057124 0.522849 0.053763 0.652554 0.121640 0.043683 0.182124 0.129704 0.000000 0.862231 0.008065 0.635081 0.051075 0.288978 0.024866 0.494624 0.120968 0.230511 0.153898 0.340054 0.010081 0.604167 0.045699 0.466398 0.090054 0.436828 0.006720 0.706989 0.081989 0.144489 0.066532 0.202957 0.000000 0.797043 0.000000 0.822581 0.002016 0.174731 0.000672 0.430108 0.097446 0.274866 0.197581 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRAGRAGAARRAGAARRAGAR MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG]AG[GA]AG[AG][ACG][GA][GA]AG[AG][AG][GA][AG]A[GA]A[AG] -------------------------------------------------------------------------------- Time 128.34 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************