******************************************************************************** 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/AT1G71450_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/AT1G71450_peak_sequences.fasta -dna -oc out/AT1G71450 -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= 9767 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= 2278372 N= 9767 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.27 C 0.23 G 0.23 T 0.27 Background letter frequencies (from file dataset with add-one prior applied): A 0.272 C 0.228 G 0.228 T 0.272 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DYGDCGGYGRHDDHD MEME-1 width = 15 sites = 9714 llr = 78056 E-value = 3.5e-345 ******************************************************************************** -------------------------------------------------------------------------------- Motif DYGDCGGYGRHDDHD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 42:3:::11332333 pos.-specific C 13::a::5:131121 probability G 3:a3:aa:7414324 matrix T 25:4:::41132232 bits 2.1 * *** 1.9 * *** 1.7 * *** 1.5 * *** Relative 1.3 * *** Entropy 1.1 * *** (11.6 bits) 0.9 * *** * 0.6 * ***** 0.4 ** ***** 0.2 ********** * 0.0 --------------- Multilevel ATGTCGGCGGAGGAG consensus GC G T ATTATA sequence T A CA CT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYGDCGGYGRHDDHD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 2141634 bayes= 9.96032 E= 3.5e-345 49 -146 42 -24 -72 51 -303 83 -1136 -1989 213 -1989 -2 -256 54 41 -1136 213 -1989 -712 -1989 -1989 213 -1989 -1989 -1989 213 -1036 -199 111 -1989 69 -89 -328 171 -173 27 -113 97 -119 32 18 -83 1 -17 -162 93 -13 20 -67 61 -46 19 0 -57 18 4 -82 62 -18 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYGDCGGYGRHDDHD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9714 E= 3.5e-345 0.380585 0.082664 0.306053 0.230698 0.164814 0.324274 0.027898 0.483014 0.000103 0.000000 0.999897 0.000000 0.268478 0.038604 0.330863 0.362055 0.000103 0.997941 0.000000 0.001956 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.999794 0.000206 0.068458 0.491559 0.000000 0.439984 0.146593 0.023574 0.748096 0.081738 0.328186 0.103974 0.448322 0.119518 0.339613 0.258390 0.128063 0.273935 0.242125 0.074223 0.434527 0.249125 0.312436 0.143195 0.347334 0.197035 0.310068 0.228742 0.153387 0.307803 0.279288 0.129607 0.351863 0.239242 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DYGDCGGYGRHDDHD MEME-1 regular expression -------------------------------------------------------------------------------- [AGT][TC]G[TGA]CGG[CT]G[GA][ATC][GTA][GA][ATC][GAT] -------------------------------------------------------------------------------- Time 126.79 secs. ******************************************************************************** ******************************************************************************** MOTIF YYTTCTYYTYCTYYTYCTYCT MEME-2 width = 21 sites = 2777 llr = 30431 E-value = 1.0e-103 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYTTCTYYTYCTYYTYCTYCT MEME-2 Description -------------------------------------------------------------------------------- Simplified A ::1::1::1::1:11::2::2 pos.-specific C 36239:662381562481562 probability G 1:1::1::21:1::1::1::2 matrix T 546718445628536626435 bits 2.1 1.9 1.7 * 1.5 * Relative 1.3 * * Entropy 1.1 * ** * * (15.8 bits) 0.9 * ***** *** ** ** 0.6 * ***** ***** ** ** 0.4 ******** *********** 0.2 ********************* 0.0 --------------------- Multilevel TCTTCTCCTTCTCCTTCTCCT consensus CTCC TT CT TTCC TTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTTCTYYTYCTYYTYCTYCT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 2083032 bayes= 11.8642 E= 1.0e-103 -269 58 -106 90 -435 137 -930 54 -118 -15 -122 109 -1808 28 -229 132 -1808 198 -1808 -145 -106 -772 -212 159 -1808 129 -345 63 -254 139 -930 38 -114 -36 -23 89 -1808 59 -206 114 -575 176 -1808 -30 -243 -210 -76 149 -270 107 -314 73 -180 133 -299 23 -152 -10 -121 113 -326 68 -1808 116 -285 175 -280 -74 -76 -134 -116 125 -339 125 -1808 66 -318 147 -241 11 -78 -47 -4 74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTTCTYYTYCTYYTYCTYCT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2777 E= 1.0e-103 0.042132 0.340655 0.109831 0.507382 0.013324 0.591286 0.000360 0.395031 0.119553 0.205618 0.097947 0.576882 0.000000 0.276197 0.046813 0.676990 0.000000 0.900612 0.000000 0.099388 0.130717 0.001080 0.052575 0.815628 0.000000 0.559597 0.020886 0.419517 0.046813 0.598848 0.000360 0.353979 0.123515 0.178250 0.194094 0.504141 0.000000 0.344256 0.054735 0.601008 0.005041 0.773497 0.000000 0.221462 0.050414 0.053295 0.134678 0.761613 0.041772 0.480375 0.025927 0.451927 0.078142 0.573641 0.028808 0.319409 0.095067 0.213540 0.098308 0.593086 0.028448 0.365862 0.000000 0.605690 0.037811 0.767015 0.032769 0.162405 0.160605 0.090385 0.102269 0.646741 0.025927 0.543392 0.000000 0.430681 0.029888 0.633417 0.042852 0.293842 0.158444 0.164206 0.222542 0.454807 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTTCTYYTYCTYYTYCTYCT MEME-2 regular expression -------------------------------------------------------------------------------- [TC][CT][TC][TC]CT[CT][CT]T[TC][CT]T[CT][CT][TC][TC]CT[CT][CT][TG] -------------------------------------------------------------------------------- Time 238.72 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************