******************************************************************************** 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/AT2G23340_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/AT2G23340_peak_sequences.fasta -dna -oc out/AT2G23340 -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= 7419 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= 1488046 N= 7419 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.277 C 0.223 G 0.223 T 0.277 Background letter frequencies (from file dataset with add-one prior applied): A 0.279 C 0.221 G 0.221 T 0.279 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HHDHHDYCACCGACA MEME-1 width = 15 sites = 7279 llr = 58935 E-value = 1.6e-502 ******************************************************************************** -------------------------------------------------------------------------------- Motif HHDHHDYCACCGACA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 333333117:::6:5 pos.-specific C 33234147:aa:2a2 probability G 112113113::a::2 matrix T 33332331::::2:1 bits 2.2 *** * 2.0 *** * 1.7 *** * 1.5 *** * Relative 1.3 *** * Entropy 1.1 **** * (11.7 bits) 0.9 ***** * 0.7 ***** * 0.4 ******* 0.2 * ********* 0.0 --------------- Multilevel TCACCTCCACCGACA consensus CTTTAAT G sequence AAGATG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDHHDYCACCGACA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1384180 bayes= 9.53277 E= 1.6e-502 -4 31 -57 13 -7 55 -75 0 30 -51 -12 9 -15 51 -66 8 -6 82 -109 -22 11 -78 27 12 -96 95 -77 10 -92 170 -185 -194 133 -1947 43 -1947 -1947 218 -1947 -1947 -1947 218 -1947 -674 -708 -1947 217 -699 112 -25 -372 -57 -553 217 -1947 -1947 83 -26 -26 -105 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDHHDYCACCGACA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7279 E= 1.6e-502 0.272153 0.274213 0.148235 0.305399 0.266795 0.322984 0.131199 0.279022 0.343591 0.154966 0.203599 0.297843 0.252370 0.313367 0.139167 0.295095 0.268306 0.388927 0.103586 0.239181 0.301827 0.128589 0.265421 0.304163 0.143701 0.427531 0.129139 0.299629 0.147960 0.717818 0.061272 0.072950 0.703119 0.000000 0.296881 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.997390 0.000000 0.002610 0.002061 0.000000 0.995741 0.002198 0.608600 0.186015 0.016761 0.188625 0.006045 0.993955 0.000000 0.000000 0.496359 0.184503 0.183954 0.135183 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDHHDYCACCGACA MEME-1 regular expression -------------------------------------------------------------------------------- [TCA][CTA][ATG][CTA][CAT][TAG][CT]C[AG]CCGACA -------------------------------------------------------------------------------- Time 128.97 secs. ******************************************************************************** ******************************************************************************** MOTIF YCKYCWCCKCCWYCKCCDCCR MEME-2 width = 21 sites = 1391 llr = 16231 E-value = 3.5e-064 ******************************************************************************** -------------------------------------------------------------------------------- Motif YCKYCWCCKCCWYCKCCDCCR MEME-2 Description -------------------------------------------------------------------------------- Simplified A :12:13:12113::2:13:13 pos.-specific C 67168:77166:68:79:79: probability G ::3::2::41:2::3::41:5 matrix T 4254153243254153:3212 bits 2.2 2.0 1.7 * 1.5 * * Relative 1.3 * * Entropy 1.1 * ** ** * ** * (16.8 bits) 0.9 ** ** ** * ** ** 0.7 ** ** ** ** ** ** ** 0.4 ** ***** ************ 0.2 ********************* 0.0 --------------------- Multilevel CCTCCTCCTCCTCCTCCGCCG consensus T GT AT GT AT GT TT A sequence A G A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCKYCWCCKCCWYCKCCDCCR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1339666 bayes= 12.2249 E= 3.5e-064 -514 140 -726 55 -241 172 -240 -63 -47 -123 19 69 -860 144 -826 52 -241 187 -248 -142 0 -1709 12 78 -1709 169 -287 -11 -160 174 -826 -70 -61 -138 67 45 -213 141 -160 -1 -90 153 -248 -67 25 -1709 -21 77 -270 134 -259 37 -293 184 -290 -94 -38 -374 30 83 -385 169 -1709 -5 -223 209 -1709 -860 6 -1709 72 31 -451 163 -147 -32 -208 199 -1709 -226 20 -826 117 -63 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCKYCWCCKCCWYCKCCDCCR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1391 E= 3.5e-064 0.007908 0.582315 0.001438 0.408339 0.052480 0.724659 0.041697 0.181165 0.202013 0.094177 0.252336 0.451474 0.000719 0.598131 0.000719 0.400431 0.052480 0.803738 0.039540 0.104242 0.278936 0.000000 0.240115 0.480949 0.000000 0.710280 0.030194 0.259526 0.092020 0.735442 0.000719 0.171819 0.182602 0.084831 0.351546 0.381021 0.063983 0.585191 0.072610 0.278217 0.149533 0.635514 0.039540 0.175413 0.332135 0.000000 0.190510 0.477354 0.043134 0.558591 0.036664 0.361610 0.036664 0.788641 0.029475 0.145219 0.214234 0.016535 0.271747 0.497484 0.019410 0.710280 0.000000 0.270309 0.059669 0.939612 0.000000 0.000719 0.291157 0.000000 0.362329 0.346513 0.012221 0.684400 0.079799 0.223580 0.066139 0.875629 0.000000 0.058231 0.321352 0.000719 0.496765 0.181165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YCKYCWCCKCCWYCKCCDCCR MEME-2 regular expression -------------------------------------------------------------------------------- [CT]C[TGA][CT]C[TAG][CT]C[TG][CT]C[TA][CT]C[TGA][CT]C[GTA][CT]C[GA] -------------------------------------------------------------------------------- Time 241.98 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************