******************************************************************************** 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/AT4G01250_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/AT4G01250_peak_sequences.fasta -dna -oc out/AT4G01250 -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= 5948 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= 1276713 N= 5948 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.333 C 0.167 G 0.167 T 0.333 Background letter frequencies (from file dataset with add-one prior applied): A 0.334 C 0.166 G 0.166 T 0.334 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAAAGTCAAMD MEME-1 width = 11 sites = 5930 llr = 51863 E-value = 1.2e-517 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5778:::aa32 pos.-specific C 21::::a::62 probability G 1112a:::::3 matrix T 222::a:::13 bits 2.6 * * 2.3 * * 2.1 * * 1.8 * * Relative 1.6 ***** Entropy 1.3 ***** (12.6 bits) 1.0 ***** 0.8 ******* 0.5 ******** 0.3 ********** 0.0 ----------- Multilevel AAAAGTCAACG consensus T AT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1217233 bayes= 9.88228 E= 1.2e-517 60 5 -49 -72 97 -111 -97 -86 116 -325 -170 -84 125 -1918 -3 -287 -936 -1918 259 -836 -936 -1918 -1918 158 -863 259 -1918 -895 157 -519 -1918 -763 156 -1918 -344 -936 0 182 -504 -223 -88 -5 107 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 5930 E= 1.2e-517 0.507420 0.171669 0.118044 0.202867 0.653288 0.077234 0.084992 0.184486 0.745025 0.017538 0.051265 0.186172 0.791737 0.000000 0.162732 0.045531 0.000506 0.000000 0.998482 0.001012 0.000506 0.000000 0.000000 0.999494 0.000843 0.998482 0.000000 0.000675 0.993761 0.004553 0.000000 0.001686 0.984148 0.000000 0.015346 0.000506 0.334739 0.589207 0.005059 0.070995 0.180776 0.161046 0.349410 0.308769 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAAAGTCAAMD MEME-1 regular expression -------------------------------------------------------------------------------- [AT]AAAGTCAA[CA][GT] -------------------------------------------------------------------------------- Time 81.21 secs. ******************************************************************************** ******************************************************************************** MOTIF TTYTYTTYTTTTTTYTTYTTY MEME-2 width = 21 sites = 1214 llr = 12148 E-value = 4.6e-038 ******************************************************************************** -------------------------------------------------------------------------------- Motif TTYTYTTYTTTTTTYTTYTTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::1::::111:::111:1:: pos.-specific C 114:43132223223113123 probability G 111:::1::1::11:111:22 matrix T 785967867677875675864 bits 2.6 2.3 2.1 1.8 Relative 1.6 Entropy 1.3 * (14.4 bits) 1.0 * **** 0.8 ******** ** ** 0.5 ************** **** 0.3 ********************* 0.0 --------------------- Multilevel TTTTTTTTTTTTTTTTTTTTT consensus C CC CC C CC C C sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTYTTYTTTTTTYTTYTTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1157753 bayes= 12.1814 E= 4.6e-038 -206 -69 -118 116 -1689 -77 -104 130 -1689 126 -24 46 -236 -1689 -449 147 -1689 116 -1689 92 -1689 97 -1689 101 -1689 -81 -121 132 -1689 100 -249 94 -206 45 -1689 105 -245 6 -32 92 -195 2 -407 114 -1689 72 -217 105 -1689 -4 -97 117 -293 36 -155 104 -151 96 -198 63 -119 -79 -38 92 -142 -46 -77 98 -311 94 -74 70 -191 -66 -1689 127 -1689 24 -9 96 -420 102 30 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTYTTYTTTTTTYTTYTTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1214 E= 4.6e-038 0.079901 0.102965 0.073311 0.743822 0.000000 0.097199 0.080725 0.822076 0.000000 0.399506 0.140857 0.459638 0.065074 0.000000 0.007414 0.927512 0.000000 0.370675 0.000000 0.629325 0.000000 0.326194 0.000000 0.673806 0.000000 0.094728 0.071664 0.833608 0.000000 0.331960 0.029654 0.638386 0.079901 0.227348 0.000000 0.692751 0.060956 0.172982 0.133443 0.632619 0.086491 0.168040 0.009885 0.735585 0.000000 0.273476 0.037068 0.689456 0.000000 0.162273 0.084843 0.752883 0.043657 0.214168 0.056837 0.685338 0.116969 0.322900 0.042010 0.518122 0.146623 0.096376 0.127677 0.629325 0.124382 0.121087 0.097199 0.657331 0.038715 0.318781 0.099671 0.542834 0.088962 0.105437 0.000000 0.805601 0.000000 0.196046 0.156507 0.647446 0.018122 0.337727 0.205107 0.439044 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TTYTYTTYTTTTTTYTTYTTY MEME-2 regular expression -------------------------------------------------------------------------------- TT[TC]T[TC][TC]T[TC][TC]TT[TC]T[TC][TC]TT[TC]TT[TCG] -------------------------------------------------------------------------------- Time 153.36 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************