******************************************************************************** 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/AT5G18270_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/AT5G18270_peak_sequences.fasta -dna -oc out/AT5G18270 -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= 5730 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= 1164964 N= 5730 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.321 C 0.179 G 0.179 T 0.321 Background letter frequencies (from file dataset with add-one prior applied): A 0.323 C 0.177 G 0.177 T 0.323 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HDKHKKTTDCTTGTWYBWCA MEME-1 width = 20 sites = 3291 llr = 25002 E-value = 1.3e-188 ******************************************************************************** -------------------------------------------------------------------------------- Motif HDKHKKTTDCTTGTWYBWCA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 322322:13:::122124:a pos.-specific C 222221::2a::3223317: probability G 122144:22:3:6122211: matrix T 444333973:7a1544342: bits 2.5 2.2 * 2.0 * 1.7 * * Relative 1.5 * * * Entropy 1.2 * * * * (11.0 bits) 1.0 * *** ** 0.7 * **** ** 0.5 ** **** ** 0.2 **** ***** ** ** 0.0 -------------------- Multilevel TTTAGGTTTCTTGTTTCACA consensus AAGTTT A G CCACTTT sequence C C G G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDKHKKTTDCTTGTWYBWCA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1056094 bayes= 10.5389 E= 1.3e-188 -35 39 -34 21 -37 -2 15 23 -71 11 24 31 7 46 -70 -7 -105 -8 110 -12 -95 -27 99 5 -275 -247 -1833 151 -119 -406 -7 107 -15 -16 37 -1 -705 247 -1833 -430 -1005 -423 71 112 -705 -423 -502 161 -208 51 167 -161 -101 24 -107 76 -49 13 -19 38 -131 88 -5 20 -99 96 19 -15 25 -59 -30 13 -323 192 -117 -57 163 -1833 -1833 -905 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDKHKKTTDCTTGTWYBWCA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 3291 E= 1.3e-188 0.252811 0.232756 0.140079 0.374354 0.249164 0.174415 0.197204 0.379216 0.197812 0.191127 0.209663 0.401398 0.339714 0.243087 0.109085 0.308113 0.155880 0.167730 0.379824 0.296566 0.167122 0.147372 0.352173 0.333333 0.048010 0.031905 0.000000 0.920085 0.141902 0.010635 0.168338 0.679125 0.289881 0.158918 0.229717 0.321483 0.002431 0.981161 0.000000 0.016408 0.000304 0.009420 0.289274 0.701003 0.002431 0.009420 0.005469 0.982680 0.076572 0.252811 0.564874 0.105743 0.160134 0.208751 0.084473 0.546642 0.229414 0.193558 0.155880 0.421149 0.130356 0.326952 0.171073 0.371620 0.162868 0.345488 0.201762 0.289881 0.384382 0.117897 0.144029 0.353692 0.034336 0.669401 0.078699 0.217563 0.999392 0.000000 0.000000 0.000608 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDKHKKTTDCTTGTWYBWCA MEME-1 regular expression -------------------------------------------------------------------------------- [TAC][TA][TG][ATC][GT][GT]TT[TAG]C[TG]T[GC][TC][TA][TC][CTG][AT][CT]A -------------------------------------------------------------------------------- Time 66.60 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTTYTTCTTYTTYTYYTTCT MEME-2 width = 21 sites = 696 llr = 7625 E-value = 4.6e-021 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTTYTTCTTYTTYTYYTTCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 1::::1::1:::::111:122 pos.-specific C 24224226:34326:333172 probability G :1111::1:::::1:112::1 matrix T 6576578397678395568:5 bits 2.5 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 * * (15.8 bits) 1.0 *** * * * * 0.7 **** ********* * 0.5 **************** *** 0.2 ********************* 0.0 --------------------- Multilevel TTTTTTTCTTTTTCTTTTTCT consensus CC CC T CCC T CCC A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTCTTYTTYTYYTTCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1050364 bayes= 12.8164 E= 4.6e-021 -135 18 -204 96 -1609 115 -99 68 -1609 -19 -63 118 -1609 37 -41 98 -781 114 -92 67 -175 4 -225 108 -1609 -2 -1609 135 -1609 186 -122 -20 -127 -536 -1609 142 -390 87 -1609 102 -1609 120 -378 84 -423 62 -225 106 -1609 -18 -1609 139 -464 174 -102 -6 -264 -219 -495 149 -211 78 -114 74 -217 87 -86 65 -1609 50 6 80 -186 -68 -195 122 -49 203 -1609 -281 -71 -23 -42 69 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTCTTYTTYTYYTTCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 696 E= 4.6e-021 0.126437 0.201149 0.043103 0.629310 0.000000 0.392241 0.089080 0.518678 0.000000 0.155172 0.114943 0.729885 0.000000 0.228448 0.133621 0.637931 0.001437 0.390805 0.093391 0.514368 0.096264 0.182471 0.037356 0.683908 0.000000 0.175287 0.000000 0.824713 0.000000 0.642241 0.076149 0.281609 0.133621 0.004310 0.000000 0.862069 0.021552 0.323276 0.000000 0.655172 0.000000 0.408046 0.012931 0.579023 0.017241 0.271552 0.037356 0.673851 0.000000 0.156609 0.000000 0.843391 0.012931 0.590517 0.087644 0.308908 0.051724 0.038793 0.005747 0.903736 0.074713 0.304598 0.080460 0.540230 0.071839 0.323276 0.097701 0.507184 0.000000 0.251437 0.185345 0.563218 0.089080 0.110632 0.045977 0.754310 0.229885 0.724138 0.000000 0.045977 0.196839 0.150862 0.132184 0.520115 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTCTTYTTYTYYTTCT MEME-2 regular expression -------------------------------------------------------------------------------- [TC][TC]T[TC][TC]TT[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[CA]T -------------------------------------------------------------------------------- Time 126.97 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************