******************************************************************************** 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/AT5G16820_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/AT5G16820_peak_sequences.fasta -dna -oc out/AT5G16820 -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= 4417 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= 920285 N= 4417 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.306 C 0.194 G 0.194 T 0.306 Background letter frequencies (from file dataset with add-one prior applied): A 0.308 C 0.192 G 0.192 T 0.308 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NTTCTAGAANCTTCT MEME-1 width = 15 sites = 4413 llr = 36500 E-value = 2.3e-480 ******************************************************************************** -------------------------------------------------------------------------------- Motif NTTCTAGAANCTTCT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 221:16:972211:1 pos.-specific C 321921:::251:92 probability G 21::12a:132:::1 matrix T 368:7::12328916 bits 2.4 2.1 * 1.9 * * 1.7 * * * Relative 1.4 * * * Entropy 1.2 * * ** (11.9 bits) 1.0 ** ** ** 0.7 ** ** *** 0.5 ******* *** 0.2 ******** ***** 0.0 --------------- Multilevel TTTCTAGAAGCTTCT consensus C TT C sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NTTCTAGAANCTTCT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 858447 bayes= 9.62287 E= 2.3e-480 -59 66 -9 2 -79 -4 -169 90 -228 -157 -252 145 -1875 226 -229 -287 -261 -22 -91 115 106 -38 -21 -279 -516 -364 233 -541 152 -272 -292 -230 116 -235 -155 -54 -64 -6 75 -7 -69 131 -34 -78 -114 -164 -279 132 -238 -225 -427 153 -401 222 -358 -219 -184 33 -90 89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NTTCTAGAANCTTCT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4413 E= 2.3e-480 0.204396 0.302969 0.180376 0.312259 0.177884 0.187174 0.059597 0.575346 0.063449 0.064582 0.033537 0.838432 0.000000 0.918423 0.039429 0.042148 0.050306 0.165647 0.102651 0.681396 0.641514 0.147519 0.166553 0.044414 0.008611 0.015409 0.968729 0.007251 0.883073 0.029232 0.025380 0.062316 0.685928 0.037616 0.065488 0.210968 0.197825 0.184682 0.324043 0.293451 0.190800 0.477680 0.152277 0.179243 0.140041 0.061863 0.027872 0.770224 0.059143 0.040335 0.009971 0.890551 0.019035 0.897349 0.016089 0.067528 0.086109 0.242465 0.102878 0.568547 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NTTCTAGAANCTTCT MEME-1 regular expression -------------------------------------------------------------------------------- [TCA]TTCTAGA[AT][GT]CTTC[TC] -------------------------------------------------------------------------------- Time 68.42 secs. ******************************************************************************** ******************************************************************************** MOTIF RARAARAAGAARAAGAAGARR MEME-2 width = 21 sites = 2252 llr = 19236 E-value = 8.5e-102 ******************************************************************************** -------------------------------------------------------------------------------- Motif RARAARAAGAARAAGAAGARR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 565654762874772662a54 pos.-specific C 1::12111111:111211::1 probability G 334225226126216118:44 matrix T 1:111:11:::::1112::11 bits 2.4 2.1 1.9 1.7 Relative 1.4 * Entropy 1.2 ** (12.3 bits) 1.0 * * ** 0.7 * ***** * ** 0.5 ** *********** *** 0.2 ********************* 0.0 --------------------- Multilevel AAAAAGAAGAAGAAGAAGAAA consensus GGGGGA A A A GG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAARAAGAARAAGAAGARR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 831945 bayes= 10.3092 E= 8.5e-102 69 -62 47 -147 104 -355 69 -301 70 -269 102 -192 89 -97 13 -136 67 -32 27 -129 34 -79 130 -358 111 -91 -32 -197 103 -147 -15 -127 -42 -117 174 -287 141 -179 -88 -368 121 -147 -17 -266 29 -253 161 -685 121 -85 -35 -325 109 -144 -48 -116 -42 -117 165 -193 106 -22 -46 -247 101 -83 -94 -85 -90 -152 198 -535 163 -1778 -876 -264 83 -211 87 -241 48 -179 95 -111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAARAAGAARAAGAAGARR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2252 E= 8.5e-102 0.496892 0.125222 0.266430 0.111456 0.634547 0.016430 0.310835 0.038188 0.498668 0.029751 0.390320 0.081261 0.571048 0.098135 0.210924 0.119893 0.488011 0.154529 0.231794 0.125666 0.388988 0.111456 0.473801 0.025755 0.664742 0.102575 0.154085 0.078597 0.629663 0.069272 0.173179 0.127886 0.229574 0.085258 0.642984 0.042185 0.815719 0.055506 0.104796 0.023979 0.711368 0.069272 0.170515 0.048845 0.377442 0.033304 0.586590 0.002664 0.710480 0.106572 0.150533 0.032416 0.653641 0.071048 0.137655 0.137655 0.229574 0.085258 0.604352 0.080817 0.640320 0.164742 0.139432 0.055506 0.621670 0.107904 0.099911 0.170515 0.165187 0.067052 0.760213 0.007549 0.950266 0.000000 0.000444 0.049290 0.547513 0.044405 0.350355 0.057726 0.430284 0.055506 0.372114 0.142096 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RARAARAAGAARAAGAAGARR MEME-2 regular expression -------------------------------------------------------------------------------- [AG][AG][AG][AG][AG][GA]AA[GA]AA[GA]AA[GA]AAGA[AG][AG] -------------------------------------------------------------------------------- Time 127.02 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************