******************************************************************************** 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/AT4G01550_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/AT4G01550_peak_sequences.fasta -dna -oc out/AT4G01550 -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= 1943 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= 453421 N= 1943 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.314 C 0.186 G 0.186 T 0.314 Background letter frequencies (from file dataset with add-one prior applied): A 0.316 C 0.184 G 0.184 T 0.316 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WMCTTSTYYNRYAAG MEME-1 width = 15 sites = 1913 llr = 17551 E-value = 6.2e-526 ******************************************************************************** -------------------------------------------------------------------------------- Motif WMCTTSTYYNRYAAG MEME-1 Description -------------------------------------------------------------------------------- Simplified A 44:::212134:a8: pos.-specific C :3a::4224325:2: probability G 11:1:3121221::a matrix T 51:9a:653324::: bits 2.4 * * 2.2 * * 2.0 * * 1.7 * * * * Relative 1.5 * * * * Entropy 1.2 *** * * (13.2 bits) 1.0 *** *** 0.7 *** **** 0.5 **** **** 0.2 ********* **** 0.0 --------------- Multilevel TACTTCTTCTACAAG consensus AC G CTCGT C sequence A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTTSTYYNRYAAG MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 426219 bayes= 9.50105 E= 6.2e-526 27 -1755 -43 61 30 85 -32 -127 -1755 244 -1755 -923 -1755 -1755 -119 154 -1755 -1755 -1755 166 -58 125 77 -311 -144 11 -116 93 -105 35 -28 55 -134 115 -51 9 -30 60 -8 -12 39 -1 28 -82 -724 145 -123 40 166 -1755 -1755 -1755 128 33 -1755 -1755 -1755 -1755 243 -592 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTTSTYYNRYAAG MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1913 E= 6.2e-526 0.381077 0.000000 0.136958 0.481965 0.389963 0.331417 0.147935 0.130685 0.000000 0.999477 0.000000 0.000523 0.000000 0.000000 0.080502 0.919498 0.000000 0.000000 0.000000 1.000000 0.210664 0.439101 0.313643 0.036592 0.116048 0.198118 0.082593 0.603241 0.152117 0.235233 0.151594 0.461056 0.124935 0.409827 0.129117 0.336121 0.256142 0.279665 0.174072 0.290120 0.414009 0.182436 0.224255 0.179300 0.002091 0.502352 0.078411 0.417146 1.000000 0.000000 0.000000 0.000000 0.768949 0.231051 0.000000 0.000000 0.000000 0.000000 0.994773 0.005227 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WMCTTSTYYNRYAAG MEME-1 regular expression -------------------------------------------------------------------------------- [TA][AC]CTT[CGA]T[TC][CT][TCA][AG][CT]A[AC]G -------------------------------------------------------------------------------- Time 73.57 secs. ******************************************************************************** ******************************************************************************** MOTIF ARAARAARAARAAGAARRAGA MEME-2 width = 21 sites = 405 llr = 4444 E-value = 6.6e-073 ******************************************************************************** -------------------------------------------------------------------------------- Motif ARAARAARAARAAGAARRAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 548746648748829754828 pos.-specific C 1:11:11:1::1111::2:11 probability G 251262261262171333:71 matrix T 211::11::1::::::1:2:: bits 2.4 2.2 2.0 1.7 Relative 1.5 Entropy 1.2 * * * * (15.8 bits) 1.0 * ** * ** ** 0.7 * * ********* *** 0.5 **** ************** 0.2 ********************* 0.0 --------------------- Multilevel AGAAGAAGAAGAAGAAAAAGA consensus A AG A A GGGT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARAARAARAAGAARRAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 414561 bayes= 12.2114 E= 6.6e-073 70 -52 -7 -79 31 -231 138 -179 129 -113 -101 -254 118 -90 -29 -319 49 -1531 159 -1531 81 -31 36 -241 96 -70 -3 -175 39 -1531 164 -500 140 -122 -105 -1531 120 -1531 10 -200 25 -1531 176 -1531 127 -118 -22 -1531 128 -118 -44 -441 -68 -122 197 -1531 146 -122 -183 -1531 114 -622 45 -268 63 -252 90 -122 48 -18 92 -275 125 -1531 -222 -61 -98 -52 195 -1531 133 -127 -55 -699 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARAARAARAAGAARRAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 405 E= 6.6e-073 0.513580 0.128395 0.175309 0.182716 0.392593 0.037037 0.479012 0.091358 0.770370 0.083951 0.091358 0.054321 0.716049 0.098765 0.150617 0.034568 0.444444 0.000000 0.555556 0.000000 0.555556 0.148148 0.237037 0.059259 0.612346 0.113580 0.180247 0.093827 0.414815 0.000000 0.575309 0.009877 0.832099 0.079012 0.088889 0.000000 0.723457 0.000000 0.197531 0.079012 0.375309 0.000000 0.624691 0.000000 0.760494 0.081481 0.158025 0.000000 0.767901 0.081481 0.135802 0.014815 0.197531 0.079012 0.723457 0.000000 0.869136 0.079012 0.051852 0.000000 0.696296 0.002469 0.251852 0.049383 0.488889 0.032099 0.343210 0.135802 0.441975 0.162963 0.348148 0.046914 0.753086 0.000000 0.039506 0.207407 0.160494 0.128395 0.711111 0.000000 0.795062 0.076543 0.125926 0.002469 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif ARAARAARAARAAGAARRAGA MEME-2 regular expression -------------------------------------------------------------------------------- A[GA]AA[GA][AG]A[GA]AA[GA]AAGA[AG][AG][AG][AT]GA -------------------------------------------------------------------------------- Time 141.55 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************