******************************************************************************** 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/AT2G42430_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/AT2G42430_peak_sequences.fasta -dna -oc out/AT2G42430 -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= 1337 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= 225677 N= 1337 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.307 C 0.193 G 0.193 T 0.307 Background letter frequencies (from file dataset with add-one prior applied): A 0.309 C 0.191 G 0.191 T 0.309 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TCCGKATTTTCCGGA MEME-1 width = 15 sites = 1060 llr = 9494 E-value = 4.7e-422 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCCGKATTTTCCGGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 11:2153:1122::4 pos.-specific C 27a121::1256:12 probability G 11:652:::121a82 matrix T 6::2327a8711::2 bits 2.4 * 2.2 * * 1.9 * * 1.7 * * Relative 1.4 * * ** Entropy 1.2 ** * ** (12.9 bits) 1.0 ** * ** 0.7 ** *** *** 0.5 **** ******** 0.2 ************** 0.0 --------------- Multilevel TCCGGATTTTCCGGA consensus TTA A sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGKATTTTCCGGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 206959 bayes= 9.90795 E= 4.7e-422 -121 -18 -45 85 -207 196 -36 -303 -445 237 -1669 -1669 -91 -149 161 -76 -187 -28 132 -14 66 -161 19 -43 -9 -420 -207 108 -555 -666 -385 166 -156 -96 -449 135 -263 -35 -164 126 -52 140 -13 -154 -102 168 -94 -118 -1669 -1669 237 -427 -340 -58 207 -283 48 -5 -2 -66 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGKATTTTCCGGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1060 E= 4.7e-422 0.133962 0.167925 0.139623 0.558491 0.073585 0.739623 0.149057 0.037736 0.014151 0.985849 0.000000 0.000000 0.165094 0.067925 0.583962 0.183019 0.084906 0.157547 0.477358 0.280189 0.489623 0.062264 0.217925 0.230189 0.290566 0.010377 0.045283 0.653774 0.006604 0.001887 0.013208 0.978302 0.104717 0.098113 0.008491 0.788679 0.050000 0.150000 0.061321 0.738679 0.215094 0.503774 0.174528 0.106604 0.152830 0.611321 0.099057 0.136792 0.000000 0.000000 0.983962 0.016038 0.029245 0.127358 0.800000 0.043396 0.431132 0.183962 0.188679 0.196226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCCGKATTTTCCGGA MEME-1 regular expression -------------------------------------------------------------------------------- TCCG[GT][ATG][TA]TTT[CA]CGGA -------------------------------------------------------------------------------- Time 120.06 secs. ******************************************************************************** ******************************************************************************** MOTIF DATTTTCCCGCCAAAAMCGTAAAHYCRTGWTTTYCCSSC MEME-2 width = 39 sites = 47 llr = 1808 E-value = 1.7e-217 ******************************************************************************** -------------------------------------------------------------------------------- Motif DATTTTCCCGCCAAAAMCGTAAAHYCRTGWTTTYCCSSC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 37::::::::::aaaa6:219a93:15:35::::::::: pos.-specific C 1:::::99a:99::::39:1:::468:2:::::49945a probability G 42:::::::a::::::::8:1:::::5:7:::::::54: matrix T 21aaaa1:::1:::::11:9::1341:8:5aaa611::: bits 2.4 2.2 ** * 1.9 *** * ** * 1.7 ************ ** *** ** * Relative 1.4 ************** ** * * *** ** * Entropy 1.2 ************** ** *** ** * *** ***** (55.5 bits) 1.0 ************** ****** ***** ********* 0.7 ************** ****** *************** 0.5 ************************************** 0.2 *************************************** 0.0 --------------------------------------- Multilevel GATTTTCCCGCCAAAAACGTAAACCCGTGTTTTTCCGCC consensus A C AT A AA C CG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DATTTTCCCGCCAAAAMCGTAAAHYCRTGWTTTYCCSSC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 39 n= 174871 bayes= 12.9433 E= 1.7e-217 -28 -84 108 -40 118 -316 -16 -154 -1220 -1220 -216 163 -386 -1220 -1220 166 -1220 -1220 -1220 169 -1220 -316 -1220 166 -1220 216 -216 -154 -1220 226 -216 -286 -1220 236 -316 -1220 -386 -1220 236 -1220 -1220 219 -216 -186 -286 226 -1220 -286 169 -1220 -1220 -1220 169 -1220 -1220 -1220 169 -1220 -1220 -1220 169 -1220 -1220 -1220 89 64 -316 -154 -1220 216 -1220 -105 -86 -1220 212 -1220 -228 -158 -1220 150 153 -216 -158 -1220 163 -1220 -216 -1220 156 -1220 -1220 -186 14 101 -1220 -16 -1220 159 -1220 46 -228 212 -216 -228 60 -1220 148 -1220 -386 1 -1220 135 -5 -1220 188 -1220 66 -1220 -1220 72 -1220 -1220 -1220 169 -1220 -1220 -1220 169 -1220 -1220 -1220 169 -1220 123 -1220 84 -1220 226 -1220 -186 -1220 230 -1220 -228 -386 123 148 -1220 -1220 148 116 -286 -1220 236 -1220 -386 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DATTTTCCCGCCAAAAMCGTAAAHYCRTGWTTTYCCSSC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 39 nsites= 47 E= 1.7e-217 0.255319 0.106383 0.404255 0.234043 0.702128 0.021277 0.170213 0.106383 0.000000 0.000000 0.042553 0.957447 0.021277 0.000000 0.000000 0.978723 0.000000 0.000000 0.000000 1.000000 0.000000 0.021277 0.000000 0.978723 0.000000 0.851064 0.042553 0.106383 0.000000 0.914894 0.042553 0.042553 0.000000 0.978723 0.021277 0.000000 0.021277 0.000000 0.978723 0.000000 0.000000 0.872340 0.042553 0.085106 0.042553 0.914894 0.000000 0.042553 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.574468 0.297872 0.021277 0.106383 0.000000 0.851064 0.000000 0.148936 0.170213 0.000000 0.829787 0.000000 0.063830 0.063830 0.000000 0.872340 0.893617 0.042553 0.063830 0.000000 0.957447 0.000000 0.042553 0.000000 0.914894 0.000000 0.000000 0.085106 0.340426 0.382979 0.000000 0.276596 0.000000 0.574468 0.000000 0.425532 0.063830 0.829787 0.042553 0.063830 0.468085 0.000000 0.531915 0.000000 0.021277 0.191489 0.000000 0.787234 0.297872 0.000000 0.702128 0.000000 0.489362 0.000000 0.000000 0.510638 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.446809 0.000000 0.553191 0.000000 0.914894 0.000000 0.085106 0.000000 0.936170 0.000000 0.063830 0.021277 0.446809 0.531915 0.000000 0.000000 0.531915 0.425532 0.042553 0.000000 0.978723 0.000000 0.021277 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DATTTTCCCGCCAAAAMCGTAAAHYCRTGWTTTYCCSSC MEME-2 regular expression -------------------------------------------------------------------------------- [GAT]ATTTTCCCGCCAAAA[AC]CGTAAA[CAT][CT]C[GA]T[GA][TA]TTT[TC]CC[GC][CG]C -------------------------------------------------------------------------------- Time 222.65 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************