******************************************************************************** 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/AT3G04030_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/AT3G04030_peak_sequences.fasta -dna -oc out/AT3G04030 -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= 8057 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= 1766670 N= 8057 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.333 C 0.167 G 0.167 T 0.333 Background letter frequencies (from file dataset with add-one prior applied): A 0.334 C 0.166 G 0.166 T 0.334 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AADRGAATCTT MEME-1 width = 11 sites = 8031 llr = 59593 E-value = 3.6e-245 ******************************************************************************** -------------------------------------------------------------------------------- Motif AADRGAATCTT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5545:aa:312 pos.-specific C 1112::::7:1 probability G 2223a:::::1 matrix T 222::::a:96 bits 2.6 * 2.3 * 2.1 * 1.8 * Relative 1.6 **** Entropy 1.3 ***** (10.7 bits) 1.0 ****** 0.8 ****** 0.5 ******* 0.3 ******** 0.0 ----------- Multilevel AAAAGAATCTT consensus TTGG A A sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AADRGAATCTT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 1686100 bayes= 9.86114 E= 3.6e-245 59 -68 5 -59 56 -105 19 -49 33 -47 49 -56 58 24 87 -793 -1962 -1962 259 -1962 158 -638 -1962 -980 158 -1962 -1962 -1962 -1138 -1962 -1962 158 -8 204 -806 -839 -153 -538 -510 139 -63 -82 -49 78 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AADRGAATCTT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 8031 E= 3.6e-245 0.503051 0.103848 0.171336 0.221766 0.492840 0.080189 0.189018 0.237953 0.420994 0.120035 0.232972 0.225999 0.499315 0.196115 0.303200 0.001370 0.000000 0.000000 1.000000 0.000000 0.997634 0.001992 0.000000 0.000374 1.000000 0.000000 0.000000 0.000000 0.000125 0.000000 0.000000 0.999875 0.317022 0.681360 0.000623 0.000996 0.115801 0.003985 0.004856 0.875358 0.215166 0.093886 0.118541 0.572407 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AADRGAATCTT MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][AGT][AG]GAAT[CA]T[TA] -------------------------------------------------------------------------------- Time 74.94 secs. ******************************************************************************** ******************************************************************************** MOTIF TCTTYTTCTTYTTCTYYYTC MEME-2 width = 20 sites = 1083 llr = 12398 E-value = 3.7e-010 ******************************************************************************** -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTCTYYYTC MEME-2 Description -------------------------------------------------------------------------------- Simplified A :11::1::11:1:::::11: pos.-specific C 27:35237:35218:45326 probability G 1111:1::11:11::::1:1 matrix T 72864773865682964473 bits 2.6 2.3 2.1 1.8 Relative 1.6 * * Entropy 1.3 * ** (16.5 bits) 1.0 * * ** * ***** 0.8 * ** *** * ***** * 0.5 *********** ***** ** 0.3 ******************** 0.0 -------------------- Multilevel TCTTCTTCTTCTTCTTCTTC consensus CT CT CTC CTCCT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTCTYYYTC MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 1613587 bayes= 12.8207 E= 3.7e-010 -350 22 -64 101 -221 202 -98 -97 -165 -191 -124 122 -1672 91 -166 93 -318 167 -749 38 -233 15 -145 104 -1672 64 -1672 115 -1672 214 -1672 -33 -160 -1672 -46 120 -254 78 -161 85 -1672 169 -1672 47 -157 32 -62 78 -1672 -75 -145 133 -307 222 -1672 -82 -314 -1672 -258 148 -650 114 -1672 92 -569 172 -324 36 -143 92 -47 40 -233 40 -274 105 -291 176 -55 -26 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTCTYYYTC MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 1083 E= 3.7e-010 0.029548 0.193906 0.106187 0.670360 0.072022 0.673130 0.084026 0.170822 0.106187 0.044321 0.070175 0.779317 0.000000 0.311173 0.052632 0.636196 0.036934 0.527239 0.000923 0.434903 0.066482 0.183749 0.060942 0.688827 0.000000 0.258541 0.000000 0.741459 0.000000 0.734072 0.000000 0.265928 0.109880 0.000000 0.120960 0.769160 0.057248 0.285319 0.054478 0.602955 0.000000 0.537396 0.000000 0.462604 0.112650 0.206833 0.108033 0.572484 0.000000 0.098800 0.060942 0.840259 0.039705 0.771006 0.000000 0.189289 0.037858 0.000000 0.027701 0.934441 0.003693 0.365651 0.000000 0.630656 0.006464 0.546630 0.017544 0.429363 0.123730 0.314866 0.120037 0.441367 0.066482 0.218837 0.024931 0.689751 0.044321 0.562327 0.113573 0.279778 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TCTTYTTCTTYTTCTYYYTC MEME-2 regular expression -------------------------------------------------------------------------------- TCT[TC][CT]T[TC][CT]T[TC][CT][TC]TCT[TC][CT][TC][TC][CT] -------------------------------------------------------------------------------- Time 142.46 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************