******************************************************************************** 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/AT5G18560_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/AT5G18560_peak_sequences.fasta -dna -oc out/AT5G18560 -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= 2689 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= 573325 N= 2689 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.247 C 0.253 G 0.253 T 0.247 Background letter frequencies (from file dataset with add-one prior applied): A 0.248 C 0.252 G 0.252 T 0.248 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WYCKCCGCCGYCDHCDYCKYC MEME-1 width = 21 sites = 2618 llr = 23064 E-value = 2.6e-492 ******************************************************************************** -------------------------------------------------------------------------------- Motif WYCKCCGCCGYCDHCDYCKYC MEME-1 Description -------------------------------------------------------------------------------- Simplified A 3111:::::112322211211 pos.-specific C 248:8a:8a:55145:55255 probability G 21:41:81:81:411411411 matrix T 44141:11:142232432232 bits 2.0 1.8 * 1.6 * * 1.4 * * Relative 1.2 ** * Entropy 1.0 * ****** (12.7 bits) 0.8 * ****** 0.6 * ****** 0.4 ********** *** 0.2 ****************** ** 0.0 --------------------- Multilevel TTCTCCGCCGCCGCCTCCGCC consensus AC G TTATAGTTTTT sequence ATATA A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYCKCCGCCGYCDHCDYCKYC MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 519545 bayes= 9.94431 E= 2.6e-492 35 -60 -73 56 -103 62 -152 70 -148 164 -778 -100 -98 -306 72 80 -343 168 -140 -172 -325 193 -1800 -417 -271 -936 170 -79 -1800 166 -199 -80 -834 194 -567 -341 -165 -1800 167 -107 -205 92 -152 60 -23 104 -248 -14 45 -200 48 0 0 65 -130 4 -7 97 -225 -18 -2 -1800 52 67 -120 106 -160 19 -86 112 -157 -11 -31 -63 68 -9 -85 85 -110 23 -91 102 -100 -11 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYCKCCGCCGYCDHCDYCKYC MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2618 E= 2.6e-492 0.316272 0.166157 0.152024 0.365546 0.121467 0.388464 0.088235 0.401833 0.088617 0.786478 0.001146 0.123759 0.125286 0.030176 0.414057 0.430481 0.022918 0.806341 0.095493 0.075248 0.025974 0.960275 0.000000 0.013751 0.037815 0.000382 0.818946 0.142857 0.000000 0.794500 0.063407 0.142093 0.000764 0.970970 0.004966 0.023300 0.078686 0.000000 0.803285 0.118029 0.059969 0.476318 0.088235 0.375477 0.211230 0.519481 0.045073 0.224217 0.337662 0.063025 0.351031 0.248281 0.247517 0.395722 0.102368 0.254393 0.235676 0.492743 0.053094 0.218487 0.243697 0.000000 0.361727 0.394576 0.108098 0.525210 0.083270 0.283422 0.136364 0.548892 0.084798 0.229947 0.200153 0.163102 0.403743 0.233002 0.137510 0.454545 0.117265 0.290680 0.132162 0.511841 0.126432 0.229565 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WYCKCCGCCGYCDHCDYCKYC MEME-1 regular expression -------------------------------------------------------------------------------- [TA][TC]C[TG]CCGCCG[CT][CTA][GAT][CTA][CAT][TGA][CT][CT][GTA][CT][CT] -------------------------------------------------------------------------------- Time 67.06 secs. ******************************************************************************** ******************************************************************************** MOTIF RCGGCGGHGRW MEME-2 width = 11 sites = 2302 llr = 16721 E-value = 1.1e-127 ******************************************************************************** -------------------------------------------------------------------------------- Motif RCGGCGGHGRW MEME-2 Description -------------------------------------------------------------------------------- Simplified A 5::1::24143 pos.-specific C 1a:19:14122 probability G 3:a8:a7:732 matrix T 1:::::12113 bits 2.0 * 1.8 ** * 1.6 ** ** 1.4 ** ** Relative 1.2 ***** Entropy 1.0 ***** (10.5 bits) 0.8 ***** 0.6 ****** * 0.4 ******** 0.2 ********** 0.0 ----------- Multilevel ACGGCGGCGAA consensus G A GT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGGCGGHGRW MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 546435 bayes= 9.68029 E= 1.1e-127 87 -91 29 -124 -373 194 -1781 -407 -1781 -1781 199 -1781 -117 -214 172 -1781 -323 188 -1781 -244 -1781 -1781 197 -425 -51 -194 145 -182 50 68 -432 -9 -98 -222 141 -75 68 -67 41 -118 46 -63 -67 45 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGGCGGHGRW MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 2302 E= 1.1e-127 0.453084 0.134666 0.307559 0.104692 0.018679 0.966551 0.000000 0.014770 0.000000 0.000000 1.000000 0.000000 0.110339 0.057341 0.832320 0.000000 0.026499 0.927889 0.000000 0.045613 0.000000 0.000000 0.986968 0.013032 0.173762 0.065595 0.690269 0.070374 0.350565 0.403997 0.012598 0.232841 0.125543 0.054301 0.672459 0.147698 0.397480 0.158992 0.334057 0.109470 0.339705 0.163336 0.158123 0.338836 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RCGGCGGHGRW MEME-2 regular expression -------------------------------------------------------------------------------- [AG]CGGCGG[CAT]G[AG][AT] -------------------------------------------------------------------------------- Time 125.99 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************