******************************************************************************** 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/AT1G09540_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/AT1G09540_peak_sequences.fasta -dna -oc out/AT1G09540 -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= 1812 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= 281636 N= 1812 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.303 C 0.197 G 0.197 T 0.303 Background letter frequencies (from file dataset with add-one prior applied): A 0.305 C 0.195 G 0.195 T 0.305 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF DDDWGGTWGGTRRRD MEME-1 width = 15 sites = 1808 llr = 14197 E-value = 1.3e-592 ******************************************************************************** -------------------------------------------------------------------------------- Motif DDDWGGTWGGTRRRD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 33231::4:::4443 pos.-specific C 1111:::1::::111 probability G 234189:1a7:6433 matrix T 433511a4:39:113 bits 2.4 * 2.1 * 1.9 * 1.7 ** * Relative 1.4 *** *** Entropy 1.2 *** *** (11.3 bits) 0.9 *** *** 0.7 *** **** 0.5 *** **** 0.2 ***** ****** 0.0 --------------- Multilevel TTGTGGTTGGTGGAA consensus AATA A T AAGG sequence GGA T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDWGGTWGGTRRRD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 256268 bayes= 8.17966 E= 1.3e-592 -9 -53 14 25 -7 -122 56 15 -53 -84 85 11 -17 -42 -127 72 -146 -1746 203 -173 -565 -1746 213 -111 -458 -476 -1746 168 23 -121 -49 46 -530 -546 234 -1746 -910 -1746 194 -28 -630 -227 -465 163 33 -263 152 -349 29 -70 100 -135 44 -72 81 -128 17 -87 52 -17 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDWGGTWGGTRRRD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1808 E= 1.3e-592 0.287058 0.134956 0.214049 0.363938 0.290929 0.083518 0.287058 0.338496 0.211283 0.108407 0.351770 0.328540 0.270465 0.146018 0.080752 0.502765 0.110619 0.000000 0.797566 0.091814 0.006084 0.000000 0.852323 0.141593 0.012721 0.007190 0.000000 0.980088 0.358407 0.084071 0.138827 0.418695 0.007743 0.004425 0.987832 0.000000 0.000553 0.000000 0.747788 0.251659 0.003872 0.040376 0.007743 0.948009 0.383296 0.031527 0.558075 0.027102 0.372235 0.119469 0.388827 0.119469 0.414823 0.117810 0.341814 0.125553 0.342367 0.106748 0.278761 0.272124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif DDDWGGTWGGTRRRD MEME-1 regular expression -------------------------------------------------------------------------------- [TAG][TAG][GTA][TA]GGT[TA]G[GT]T[GA][GA][AG][AGT] -------------------------------------------------------------------------------- Time 127.43 secs. ******************************************************************************** ******************************************************************************** MOTIF WCCDCMACCRCMACCRCCRC MEME-2 width = 20 sites = 137 llr = 1858 E-value = 3.3e-043 ******************************************************************************** -------------------------------------------------------------------------------- Motif WCCDCMACCRCMACCRCCRC MEME-2 Description -------------------------------------------------------------------------------- Simplified A 4124:47:23147125:251 pos.-specific C 288196:97:85:88:a7:5 probability G 2:13::3::5111::3::32 matrix T 31:21::1121:2111:121 bits 2.4 * 2.1 * 1.9 * * 1.7 * * * Relative 1.4 * * * * Entropy 1.2 ** * ** * ** * (19.6 bits) 0.9 ** ***** ** ** ** 0.7 ** ***** ** ** ** 0.5 ** **************** 0.2 ******************* 0.0 -------------------- Multilevel ACCACCACCGCCACCACCAC consensus T G AG A A G G sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCDCMACCRCMACCRCCRC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 247208 bayes= 13.0572 E= 3.3e-043 29 -28 -21 -3 -122 199 -1374 -169 -69 196 -193 -1374 20 -142 82 -39 -280 216 -473 -193 31 162 -1374 -380 118 -1374 62 -538 -1374 221 -1374 -158 -93 193 -241 -239 14 -1374 133 -80 -180 202 -174 -222 45 145 -193 -1374 114 -1374 -49 -69 -114 204 -1374 -239 -86 200 -1374 -258 82 -1374 75 -122 -1374 235 -1374 -538 -80 186 -1374 -139 72 -1374 58 -58 -106 143 -4 -114 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCDCMACCRCMACCRCCRC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 137 E= 3.3e-043 0.372263 0.160584 0.167883 0.299270 0.131387 0.773723 0.000000 0.094891 0.189781 0.759124 0.051095 0.000000 0.350365 0.072993 0.343066 0.233577 0.043796 0.868613 0.007299 0.080292 0.379562 0.598540 0.000000 0.021898 0.693431 0.000000 0.299270 0.007299 0.000000 0.897810 0.000000 0.102190 0.160584 0.744526 0.036496 0.058394 0.335766 0.000000 0.489051 0.175182 0.087591 0.788321 0.058394 0.065693 0.416058 0.532847 0.051095 0.000000 0.671533 0.000000 0.138686 0.189781 0.138686 0.802920 0.000000 0.058394 0.167883 0.781022 0.000000 0.051095 0.540146 0.000000 0.328467 0.131387 0.000000 0.992701 0.000000 0.007299 0.175182 0.708029 0.000000 0.116788 0.503650 0.000000 0.291971 0.204380 0.145985 0.525547 0.189781 0.138686 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WCCDCMACCRCMACCRCCRC MEME-2 regular expression -------------------------------------------------------------------------------- [AT]CC[AGT]C[CA][AG]CC[GA]C[CA]ACC[AG]CC[AGT]C -------------------------------------------------------------------------------- Time 232.89 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************