******************************************************************************** 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/AT3G22830_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/AT3G22830_peak_sequences.fasta -dna -oc out/AT3G22830 -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= 4454 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= 713758 N= 4454 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.309 C 0.191 G 0.191 T 0.309 Background letter frequencies (from file dataset with add-one prior applied): A 0.31 C 0.19 G 0.19 T 0.31 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HTTCTAGAANHTTCT MEME-1 width = 15 sites = 4444 llr = 36305 E-value = 2.9e-696 ******************************************************************************** -------------------------------------------------------------------------------- Motif HTTCTAGAANHTTCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 221::6:862221:1 pos.-specific C 32:a211:1241:92 probability G 21::129:132:::1 matrix T 369:71:123279:6 bits 2.4 2.2 * 1.9 * * 1.7 * * * Relative 1.4 * * * Entropy 1.2 ** * * (11.8 bits) 1.0 ** ** ** 0.7 ** ** ** 0.5 ****** *** 0.2 ******** ***** 0.0 --------------- Multilevel TTTCTAGAATCTTCT consensus C TGT C sequence A AA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTTCTAGAANHTTCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 651402 bayes= 8.96779 E= 2.9e-696 -45 54 -25 12 -93 -21 -174 99 -246 -336 -295 154 -1876 237 -318 -1043 -317 -13 -91 116 103 -35 -27 -235 -441 -160 225 -392 144 -281 -235 -173 99 -185 -96 -40 -48 -3 42 12 -51 109 -30 -47 -99 -149 -240 125 -233 -256 -278 150 -884 229 -261 -295 -197 16 -55 90 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTTCTAGAANHTTCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4444 E= 2.9e-696 0.226598 0.275653 0.159316 0.338434 0.162916 0.163591 0.056706 0.616787 0.056256 0.018452 0.024527 0.900765 0.000000 0.978848 0.020927 0.000225 0.034428 0.173042 0.100585 0.691944 0.633663 0.148290 0.157291 0.060756 0.014626 0.062331 0.902565 0.020477 0.842034 0.027003 0.037129 0.093834 0.614761 0.052655 0.097210 0.235374 0.223222 0.185194 0.254275 0.337309 0.218047 0.403465 0.153915 0.224572 0.156166 0.067282 0.036004 0.740549 0.061656 0.032178 0.027678 0.878488 0.000675 0.928218 0.031053 0.040054 0.079433 0.212196 0.129388 0.578983 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTTCTAGAANHTTCT MEME-1 regular expression -------------------------------------------------------------------------------- [TCA]TTCTAGA[AT][TGA][CTA]TTC[TC] -------------------------------------------------------------------------------- Time 82.01 secs. ******************************************************************************** ******************************************************************************** MOTIF ARAARARGAAGAARAAGARRR MEME-2 width = 21 sites = 559 llr = 6614 E-value = 9.4e-060 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARAARARGAAGAARAAGARRR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 6365375379:9637818555 pos.-specific C 1111:111:::11::::1::1 probability G 2523613631a:372181353 matrix T 21:1:11:::::1::1::1:1 bits 2.4 2.2 * 1.9 * 1.7 * * Relative 1.4 * * Entropy 1.2 *** * * (17.1 bits) 1.0 * ***** ***** 0.7 * * ***** ***** * 0.5 ** ** ************* 0.2 ********************* 0.0 --------------------- Multilevel AGAAGAAGAAGAAGAAGAAAA consensus AGGA GAG GAG GGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARARGAAGAARAAGARRR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 624678 bayes= 12.3674 E= 9.4e-060 83 -64 -24 -92 9 -192 150 -192 102 -54 34 -1577 81 -117 47 -151 12 -233 172 -1577 114 -111 -60 -161 74 -124 56 -133 -6 -182 178 -1577 120 -314 49 -1577 150 -1577 -62 -1577 -1577 -340 233 -344 151 -130 -1577 -312 85 -95 50 -205 12 -1577 180 -1577 124 -264 33 -1577 142 -1577 -77 -244 -149 -227 216 -1577 141 -173 -120 -312 73 -220 85 -158 63 -303 126 -292 61 -48 56 -149 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARARGAAGAARAAGARRR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 559 E= 9.4e-060 0.552773 0.121646 0.161002 0.164580 0.330948 0.050089 0.536673 0.082290 0.629696 0.130590 0.239714 0.000000 0.543828 0.084079 0.262970 0.109123 0.336315 0.037567 0.626118 0.000000 0.685152 0.087657 0.125224 0.101968 0.516995 0.080501 0.279070 0.123435 0.296959 0.053667 0.649374 0.000000 0.711986 0.021467 0.266547 0.000000 0.876565 0.000000 0.123435 0.000000 0.000000 0.017889 0.953488 0.028623 0.887299 0.076923 0.000000 0.035778 0.558140 0.098390 0.268336 0.075134 0.338104 0.000000 0.661896 0.000000 0.731664 0.030411 0.237925 0.000000 0.831843 0.000000 0.110912 0.057245 0.110912 0.039356 0.849732 0.000000 0.824687 0.057245 0.082290 0.035778 0.513417 0.041145 0.341682 0.103757 0.481216 0.023256 0.454383 0.041145 0.474061 0.135957 0.279070 0.110912 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARARGAAGAARAAGARRR MEME-2 regular expression -------------------------------------------------------------------------------- A[GA][AG][AG][GA]A[AG][GA][AG]AGA[AG][GA][AG]AGA[AG][AG][AG] -------------------------------------------------------------------------------- Time 145.02 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************