******************************************************************************** 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/AT3G10580_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/AT3G10580_peak_sequences.fasta -dna -oc out/AT3G10580 -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= 1901 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= 329469 N= 1901 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.35 C 0.15 G 0.15 T 0.35 Background letter frequencies (from file dataset with add-one prior applied): A 0.352 C 0.148 G 0.148 T 0.352 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF WAYCTTATCYWWWWH MEME-1 width = 15 sites = 1780 llr = 13268 E-value = 4.2e-278 ******************************************************************************** -------------------------------------------------------------------------------- Motif WAYCTTATCYWWWWH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 5612:1a::144544 pos.-specific C 1:55::::a412:12 probability G 1111::::::11::1 matrix T 334299:a:443553 bits 2.8 * 2.5 * 2.2 * 1.9 * Relative 1.7 * Entropy 1.4 *** (10.8 bits) 1.1 ***** 0.8 ***** 0.6 ******** 0.3 ********* * 0.0 --------------- Multilevel AACCTTATCCTAATA consensus TTT TATTAT sequence C C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAYCTTATCYWWWWH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 302855 bayes= 9.07425 E= 4.2e-278 51 -17 -90 -29 77 -188 -97 -32 -246 164 -154 26 -107 181 -31 -88 -351 -249 -1744 142 -221 -1744 -604 139 151 -1744 -1744 -1744 -1744 -572 -1744 150 -1744 275 -1744 -1744 -187 160 -352 33 10 -30 -99 28 27 48 -111 -23 48 -176 -396 38 11 -13 -237 38 3 69 -94 -12 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAYCTTATCYWWWWH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1780 E= 4.2e-278 0.500000 0.132022 0.079775 0.288202 0.601124 0.040449 0.075843 0.282584 0.064045 0.463483 0.051124 0.421348 0.167978 0.521910 0.119663 0.190449 0.030899 0.026404 0.000000 0.942697 0.075843 0.000000 0.002247 0.921910 1.000000 0.000000 0.000000 0.000000 0.000000 0.002809 0.000000 0.997191 0.000000 1.000000 0.000000 0.000000 0.096067 0.448315 0.012921 0.442697 0.377528 0.120787 0.074719 0.426966 0.424157 0.207303 0.068539 0.300000 0.489888 0.043820 0.009551 0.456742 0.379213 0.135955 0.028652 0.456180 0.359551 0.239326 0.077528 0.323596 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WAYCTTATCYWWWWH MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AT][CT]CTTATC[CT][TA][ATC][AT][TA][ATC] -------------------------------------------------------------------------------- Time 77.70 secs. ******************************************************************************** ******************************************************************************** MOTIF YYTYHTCTTYTTYTTYTTYTTHTYYHTY MEME-2 width = 28 sites = 161 llr = 1892 E-value = 6.5e-020 ******************************************************************************** -------------------------------------------------------------------------------- Motif YYTYHTCTTYTTYTTYTTYTTHTYYHTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A :21:31:11:1::1:12::2:21:2321 pos.-specific C 6334217235116225235133163223 probability G :::11:11::11:1::11:1:1111::2 matrix T 4566482675784683665673734564 bits 2.8 2.5 2.2 1.9 Relative 1.7 Entropy 1.4 * * (17.0 bits) 1.1 * * * * * * 0.8 * * * ** * ** ** * * 0.6 * ** ** ** ** ** ** * ** 0.3 **** ************** ******** 0.0 ---------------------------- Multilevel CTTTTTCTTCTTCTTCTTTTTCTCTTTT consensus TCCCA CCT TCCT CCACT TCAAC sequence A C A AC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTYHTCTTYTTYTTYTTYTTHTYYHTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 28 n= 278142 bayes= 12.5934 E= 6.5e-020 -1397 190 -177 20 -65 85 -1397 53 -150 85 -458 78 -1397 140 -141 65 -21 47 -41 11 -212 -58 -226 117 -1397 228 -77 -87 -212 63 -49 73 -265 85 -1397 95 -1397 178 -1397 48 -136 -12 -126 92 -301 -49 -99 114 -1397 211 -1397 4 -192 47 -77 81 -1397 47 -199 111 -136 181 -1397 -4 -87 7 -58 65 -1397 95 -88 85 -1397 174 -1397 52 -57 -49 -58 67 -1397 98 -258 96 -61 120 -19 -24 -265 -33 -41 102 -1397 190 1 -24 -78 112 -141 24 -21 67 -1397 39 -57 23 -1397 75 -136 85 12 31 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTYHTCTTYTTYTTYTTYTTHTYYHTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 28 nsites= 161 E= 6.5e-020 0.000000 0.552795 0.043478 0.403727 0.223602 0.267081 0.000000 0.509317 0.124224 0.267081 0.006211 0.602484 0.000000 0.391304 0.055901 0.552795 0.304348 0.204969 0.111801 0.378882 0.080745 0.099379 0.031056 0.788820 0.000000 0.720497 0.086957 0.192547 0.080745 0.229814 0.105590 0.583851 0.055901 0.267081 0.000000 0.677019 0.000000 0.509317 0.000000 0.490683 0.136646 0.136646 0.062112 0.664596 0.043478 0.105590 0.074534 0.776398 0.000000 0.639752 0.000000 0.360248 0.093168 0.204969 0.086957 0.614907 0.000000 0.204969 0.037267 0.757764 0.136646 0.521739 0.000000 0.341615 0.192547 0.155280 0.099379 0.552795 0.000000 0.285714 0.080745 0.633540 0.000000 0.496894 0.000000 0.503106 0.236025 0.105590 0.099379 0.559006 0.000000 0.291925 0.024845 0.683230 0.229814 0.341615 0.130435 0.298137 0.055901 0.118012 0.111801 0.714286 0.000000 0.552795 0.149068 0.298137 0.204969 0.322981 0.055901 0.416149 0.304348 0.236025 0.000000 0.459627 0.236025 0.173913 0.000000 0.590062 0.136646 0.267081 0.161491 0.434783 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YYTYHTCTTYTTYTTYTTYTTHTYYHTY MEME-2 regular expression -------------------------------------------------------------------------------- [CT][TCA][TC][TC][TAC]TC[TC][TC][CT]TT[CT][TC][TC][CT]T[TC][TC][TA][TC][CTA]T[CT][TCA][TAC][TA][TC] -------------------------------------------------------------------------------- Time 138.69 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************