******************************************************************************** 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/AT1G69180_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/AT1G69180_peak_sequences.fasta -dna -oc out/AT1G69180 -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= 1844 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= 417108 N= 1844 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.368 C 0.132 G 0.132 T 0.368 Background letter frequencies (from file dataset with add-one prior applied): A 0.368 C 0.132 G 0.132 T 0.368 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WHTWATCATA MEME-1 width = 10 sites = 1833 llr = 11844 E-value = 6.9e-066 ******************************************************************************** -------------------------------------------------------------------------------- Motif WHTWATCATA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 4215a1:a:6 pos.-specific C 121:::a::2 probability G 121::::::1 matrix T 3475:9::a2 bits 2.9 * 2.6 * 2.3 * 2.0 * Relative 1.8 * Entropy 1.5 * *** (9.3 bits) 1.2 ***** 0.9 ***** 0.6 ***** 0.3 ******** 0.0 ---------- Multilevel ATTAATCATA consensus TC T sequence A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WHTWATCATA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 400512 bayes= 9.11985 E= 6.9e-066 26 5 -7 -31 -71 80 24 8 -133 -66 -87 92 45 -345 -1748 39 144 -1748 -1748 -939 -276 -633 -633 135 -1748 293 -1748 -1748 144 -1748 -1748 -1748 -939 -591 -791 144 63 20 -7 -125 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WHTWATCATA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 1833 E= 6.9e-066 0.442444 0.135843 0.125477 0.296236 0.225859 0.229678 0.154937 0.389525 0.146208 0.083470 0.072013 0.698309 0.504092 0.012002 0.000000 0.483906 0.999454 0.000000 0.000000 0.000546 0.054555 0.001637 0.001637 0.942171 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000546 0.002182 0.000546 0.996727 0.568467 0.151664 0.125477 0.154392 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WHTWATCATA MEME-1 regular expression -------------------------------------------------------------------------------- [AT][TCA]T[AT]ATCATA -------------------------------------------------------------------------------- Time 117.34 secs. ******************************************************************************** ******************************************************************************** MOTIF YATGTTAAAWMATATKDTATCGCGATAAV MEME-2 width = 29 sites = 13 llr = 315 E-value = 3.3e-007 ******************************************************************************** -------------------------------------------------------------------------------- Motif YATGTTAAAWMATATKDTATCGCGATAAV MEME-2 Description -------------------------------------------------------------------------------- Simplified A :81:1:aa8537:9123:a::2::81aa4 pos.-specific C 6:2::1::21512:::::::8:8:::::3 probability G :217::::::22:1:55::2281a1:::3 matrix T 4:7399:::51:8:932a:8::2:19::: bits 2.9 * 2.6 * 2.3 * * 2.0 * * Relative 1.8 **** Entropy 1.5 * * ** ** **** ** (35.0 bits) 1.2 ** ****** ** ******* *** 0.9 ** ****** ***** ************ 0.6 ** ****** ******************* 0.3 ***************************** 0.0 ----------------------------- Multilevel CATGTTAAAACATATGGTATCGCGATAAA consensus T T TAGC TA A C sequence T G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATGTTAAAWMATATKDTATCGCGATAAV MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 365476 bayes= 15.3095 E= 3.3e-007 -1035 222 -1035 6 120 -1035 23 -1035 -226 23 -77 91 -1035 -1035 239 -26 -226 -1035 -1035 132 -1035 -77 -1035 132 144 -1035 -1035 -1035 144 -1035 -1035 -1035 120 23 -1035 -1035 32 -77 -1035 32 -26 181 23 -226 91 -77 81 -1035 -1035 81 -1035 106 132 -1035 -77 -1035 -226 -1035 -1035 132 -126 -1035 203 -26 -26 -1035 181 -67 -1035 -1035 -1035 144 144 -1035 -1035 -1035 -1035 -1035 23 120 -1035 268 23 -1035 -67 -1035 255 -1035 -1035 255 -77 -126 -1035 -1035 292 -1035 120 -1035 -77 -226 -226 -1035 -1035 132 144 -1035 -1035 -1035 144 -1035 -1035 -1035 6 122 122 -1035 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATGTTAAAWMATATKDTATCGCGATAAV MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 13 E= 3.3e-007 0.000000 0.615385 0.000000 0.384615 0.846154 0.000000 0.153846 0.000000 0.076923 0.153846 0.076923 0.692308 0.000000 0.000000 0.692308 0.307692 0.076923 0.000000 0.000000 0.923077 0.000000 0.076923 0.000000 0.923077 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.846154 0.153846 0.000000 0.000000 0.461538 0.076923 0.000000 0.461538 0.307692 0.461538 0.153846 0.076923 0.692308 0.076923 0.230769 0.000000 0.000000 0.230769 0.000000 0.769231 0.923077 0.000000 0.076923 0.000000 0.076923 0.000000 0.000000 0.923077 0.153846 0.000000 0.538462 0.307692 0.307692 0.000000 0.461538 0.230769 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.153846 0.846154 0.000000 0.846154 0.153846 0.000000 0.230769 0.000000 0.769231 0.000000 0.000000 0.769231 0.076923 0.153846 0.000000 0.000000 1.000000 0.000000 0.846154 0.000000 0.076923 0.076923 0.076923 0.000000 0.000000 0.923077 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.384615 0.307692 0.307692 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YATGTTAAAWMATATKDTATCGCGATAAV MEME-2 regular expression -------------------------------------------------------------------------------- [CT]AT[GT]TTAAA[AT][CA][AG][TC]AT[GT][GAT]TATC[GA]CGATAA[ACG] -------------------------------------------------------------------------------- Time 224.16 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************