******************************************************************************** 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/AT2G02820_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/AT2G02820_peak_sequences.fasta -dna -oc out/AT2G02820 -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= 1509 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= 196779 N= 1509 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.266 C 0.234 G 0.234 T 0.266 Background letter frequencies (from file dataset with add-one prior applied): A 0.268 C 0.232 G 0.232 T 0.268 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF NACGCKCCWYY MEME-1 width = 11 sites = 1491 llr = 12566 E-value = 1.2e-938 ******************************************************************************** -------------------------------------------------------------------------------- Motif NACGCKCCWYY MEME-1 Description -------------------------------------------------------------------------------- Simplified A 28::::::322 pos.-specific C 319:a:a9144 probability G 211a:3::111 matrix T 2::::7:1433 bits 2.1 ** * 1.9 ** * 1.7 *** ** 1.5 *** ** Relative 1.3 *** ** Entropy 1.1 ******* (12.2 bits) 0.8 ******* 0.6 ******* 0.4 ******* 0.2 ********** 0.0 ----------- Multilevel CACGCTCCTCC consensus G G ATT sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NACGCKCCWYY MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 181689 bayes= 7.99828 E= 1.2e-938 -46 56 1 -23 161 -98 -215 -425 -664 200 -178 -1719 -705 -1719 210 -1719 -1719 210 -843 -1719 -605 -1719 55 129 -1719 211 -1719 -1719 -1719 195 -527 -152 16 -74 -91 71 -49 91 -126 5 -52 70 -109 29 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NACGCKCCWYY MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 1491 E= 1.2e-938 0.195171 0.343394 0.233400 0.228035 0.815560 0.118042 0.052314 0.014085 0.002683 0.929577 0.067740 0.000000 0.002012 0.000000 0.997988 0.000000 0.000000 0.999329 0.000671 0.000000 0.004024 0.000000 0.341382 0.654594 0.000000 1.000000 0.000000 0.000000 0.000000 0.900738 0.006036 0.093226 0.298457 0.138833 0.124078 0.438632 0.190476 0.435278 0.097250 0.276995 0.187123 0.376928 0.109323 0.326626 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NACGCKCCWYY MEME-1 regular expression -------------------------------------------------------------------------------- [CGT]ACGC[TG]CC[TA][CT][CT] -------------------------------------------------------------------------------- Time 127.47 secs. ******************************************************************************** ******************************************************************************** MOTIF YYTYYTCCTYCTCYHTCTYYYYCTYYTCY MEME-2 width = 29 sites = 152 llr = 1861 E-value = 6.2e-051 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYTYYTCCTYCTCYHTCTYYYYCTYYTCY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 111111122::1::21121:1:::::111 pos.-specific C 44154265258:75227:65337156164 probability G 2112::1::1:1::22:1::11:1111:1 matrix T 34835622552834452734662844624 bits 2.1 1.9 1.7 1.5 Relative 1.3 Entropy 1.1 *** ** (17.7 bits) 0.8 * **** **** 0.6 * * * ***** **** **** * 0.4 ** ********** ************* 0.2 ************** ************** 0.0 ----------------------------- Multilevel CCTCTTCCTTCTCCTTCTCCTTCTCCTCT consensus TT TCCTTAC TTAC ATTCCT TT TC sequence AC CG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTYYTCCTYCTCYHTCTYYYYCTYYTCY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 29 n= 154527 bayes= 11.8041 E= 6.2e-051 -102 61 -50 38 -235 92 -156 68 -218 -182 -89 149 -154 107 -50 -6 -202 88 -256 80 -95 -10 -414 124 -102 138 -214 -35 -26 120 -1389 -14 -35 -14 -233 99 -1389 97 -144 78 -335 172 -233 -70 -154 -1389 -114 158 -1389 160 -282 -2 -302 120 -1389 70 -22 -6 -56 54 -202 3 -14 86 -110 153 -314 -59 -26 -414 -156 135 -235 130 -256 33 -254 111 -256 63 -218 53 -214 105 -434 32 -68 105 -254 168 -1389 -35 -534 -124 -114 156 -1389 120 -182 58 -534 128 -214 49 -89 -156 -68 124 -144 147 -414 -14 -154 76 -182 74 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTYYTCCTYCTCYHTCTYYYYCTYYTCY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 29 nsites= 152 E= 6.2e-051 0.131579 0.355263 0.164474 0.348684 0.052632 0.440789 0.078947 0.427632 0.059211 0.065789 0.125000 0.750000 0.092105 0.486842 0.164474 0.256579 0.065789 0.427632 0.039474 0.467105 0.138158 0.217105 0.013158 0.631579 0.131579 0.605263 0.052632 0.210526 0.223684 0.532895 0.000000 0.243421 0.210526 0.210526 0.046053 0.532895 0.000000 0.453947 0.085526 0.460526 0.026316 0.763158 0.046053 0.164474 0.092105 0.000000 0.105263 0.802632 0.000000 0.703947 0.032895 0.263158 0.032895 0.532895 0.000000 0.434211 0.230263 0.223684 0.157895 0.388158 0.065789 0.236842 0.210526 0.486842 0.125000 0.671053 0.026316 0.177632 0.223684 0.013158 0.078947 0.684211 0.052632 0.572368 0.039474 0.335526 0.046053 0.500000 0.039474 0.414474 0.059211 0.335526 0.052632 0.552632 0.013158 0.289474 0.144737 0.552632 0.046053 0.743421 0.000000 0.210526 0.006579 0.098684 0.105263 0.789474 0.000000 0.532895 0.065789 0.401316 0.006579 0.565789 0.052632 0.375000 0.144737 0.078947 0.144737 0.631579 0.098684 0.644737 0.013158 0.243421 0.092105 0.394737 0.065789 0.447368 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTYYTCCTYCTCYHTCTYYYYCTYYTCY MEME-2 regular expression -------------------------------------------------------------------------------- [CT][CT]T[CT][TC][TC][CT][CTA][TAC][TC]CT[CT][CT][TAC][TCG]C[TA][CT][CT][TC][TC][CT]T[CT][CT]T[CT][TC] -------------------------------------------------------------------------------- Time 231.12 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************