******************************************************************************** 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/AT5G25190_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/AT5G25190_peak_sequences.fasta -dna -oc out/AT5G25190 -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= 1551 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= 235575 N= 1551 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.231 C 0.269 G 0.269 T 0.231 Background letter frequencies (from file dataset with add-one prior applied): A 0.232 C 0.268 G 0.268 T 0.232 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF CTCCDCCGCCG MEME-1 width = 11 sites = 1414 llr = 11043 E-value = 4.0e-513 ******************************************************************************** -------------------------------------------------------------------------------- Motif CTCCDCCGCCG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 12::3::1::2 pos.-specific C 6169:aa:8a: probability G :21:4::8::7 matrix T 353:3:::1:1 bits 2.1 1.9 * 1.7 ** * 1.5 * ** * Relative 1.3 * *** * Entropy 1.1 * *** * (11.3 bits) 0.8 * ****** 0.6 ** ****** 0.4 *********** 0.2 *********** 0.0 ----------- Multilevel CTCCGCCGCCG consensus TAT A sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCDCCGCCG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 220065 bayes= 8.30756 E= 4.0e-513 -65 106 -304 16 4 -223 -41 112 -274 119 -170 22 -304 180 -524 -280 41 -1711 66 21 -736 183 -278 -536 -1711 190 -756 -1711 -81 -1711 165 -319 -227 153 -257 -80 -555 183 -1711 -240 -24 -557 144 -173 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCDCCGCCG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1414 E= 4.0e-513 0.147808 0.560820 0.032532 0.258840 0.237624 0.057284 0.202263 0.502829 0.034653 0.613154 0.082744 0.269448 0.028289 0.931400 0.007072 0.033239 0.309052 0.000000 0.422207 0.268741 0.001414 0.954031 0.038897 0.005658 0.000000 0.998586 0.001414 0.000000 0.132249 0.000000 0.842291 0.025460 0.048091 0.773692 0.045262 0.132956 0.004950 0.951202 0.000000 0.043847 0.196605 0.005658 0.727723 0.070014 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif CTCCDCCGCCG MEME-1 regular expression -------------------------------------------------------------------------------- [CT][TAG][CT]C[GAT]CCGCCG -------------------------------------------------------------------------------- Time 69.63 secs. ******************************************************************************** ******************************************************************************** MOTIF GHGGHGGYGGHGGWG MEME-2 width = 15 sites = 576 llr = 5521 E-value = 5.5e-170 ******************************************************************************** -------------------------------------------------------------------------------- Motif GHGGHGGYGGHGGWG MEME-2 Description -------------------------------------------------------------------------------- Simplified A 23:24122:22::41 pos.-specific C 13::2::5::4::2: probability G 7:98:76:98:aa:8 matrix T :41:42131:4::41 bits 2.1 1.9 1.7 ** 1.5 ** Relative 1.3 * * ** Entropy 1.1 ** ** ** * (13.8 bits) 0.8 ** * ** ** * 0.6 * ** ** ** **** 0.4 *************** 0.2 *************** 0.0 --------------- Multilevel GTGGTGGCGGTGGTG consensus C A AT C A sequence A C A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHGGHGGYGGHGGWG MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 213861 bayes= 10.7055 E= 5.5e-170 -33 -181 139 -260 16 33 -469 77 -225 -1581 174 -206 -51 -568 160 -360 70 -36 -527 82 -125 -568 138 -23 0 -310 124 -118 -8 78 -727 46 -374 -527 175 -170 -36 -1581 155 -281 -2 50 -1581 76 -1581 -381 187 -1581 -336 -568 186 -1581 75 -56 -1581 89 -131 -1581 160 -131 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHGGHGGYGGHGGWG MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 576 E= 5.5e-170 0.184028 0.076389 0.701389 0.038194 0.258681 0.336806 0.010417 0.394097 0.048611 0.000000 0.895833 0.055556 0.163194 0.005208 0.812500 0.019097 0.376736 0.208333 0.006944 0.407986 0.097222 0.005208 0.699653 0.197917 0.232639 0.031250 0.633681 0.102431 0.218750 0.460069 0.001736 0.319444 0.017361 0.006944 0.904514 0.071181 0.180556 0.000000 0.786458 0.032986 0.229167 0.378472 0.000000 0.392361 0.000000 0.019097 0.980903 0.000000 0.022569 0.005208 0.972222 0.000000 0.388889 0.182292 0.000000 0.428819 0.093750 0.000000 0.812500 0.093750 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GHGGHGGYGGHGGWG MEME-2 regular expression -------------------------------------------------------------------------------- G[TCA]GG[TAC]G[GA][CTA]GG[TCA]GG[TA]G -------------------------------------------------------------------------------- Time 130.70 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************