******************************************************************************** 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/AT1G20980_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/AT1G20980_peak_sequences.fasta -dna -oc out/AT1G20980 -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= 2585 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= 522066 N= 2585 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.313 C 0.187 G 0.187 T 0.313 Background letter frequencies (from file dataset with add-one prior applied): A 0.315 C 0.185 G 0.185 T 0.315 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGTACGGA MEME-1 width = 8 sites = 2549 llr = 21363 E-value = 1.2e-519 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGTACGGA MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1::a::16 pos.-specific C 2:::a::1 probability G 1a:::98: matrix T 5:a:::12 bits 2.4 * * 2.2 * * 1.9 * ** 1.7 ***** Relative 1.5 ****** Entropy 1.2 ****** (12.1 bits) 1.0 ****** 0.7 ****** 0.5 ******* 0.2 ******** 0.0 -------- Multilevel TGTACGGA consensus C T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTACGGA MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 8 n= 503971 bayes= 9.80952 E= 1.2e-519 -114 17 -53 72 -525 -1796 242 -1796 -1796 -1796 -1796 167 167 -1796 -1796 -1796 -1796 243 -1796 -1796 -306 -1796 231 -289 -165 -1796 216 -216 103 -85 -346 -41 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTACGGA MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 8 nsites= 2549 E= 1.2e-519 0.143193 0.208709 0.128678 0.519419 0.008239 0.000000 0.991761 0.000000 0.000000 0.000000 0.000000 1.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.037662 0.000000 0.919969 0.042370 0.100039 0.000000 0.829737 0.070224 0.643390 0.103178 0.016869 0.236563 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGTACGGA MEME-1 regular expression -------------------------------------------------------------------------------- [TC]GTACGG[AT] -------------------------------------------------------------------------------- Time 120.89 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTYTYTYTYTYTTTYTYWYT MEME-2 width = 21 sites = 555 llr = 5828 E-value = 5.5e-049 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTYTYTYTYTYTTTYTYWYT MEME-2 Description -------------------------------------------------------------------------------- Simplified A 11:::::1::1::11:::311 pos.-specific C 2434:62333:5223325132 probability G 1::1:::1:1::1::1:2111 matrix T 6575a3767595776584655 bits 2.4 2.2 1.9 1.7 Relative 1.5 * Entropy 1.2 * * (15.1 bits) 1.0 * *** * * 0.7 ***** * ******** 0.5 ****************** 0.2 ********************* 0.0 --------------------- Multilevel TTTTTCTTTTTCTTTTTCTTT consensus CCCC TCCCC TC CC TACC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTYTYTYTYTTTYTYWYT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 470366 bayes= 11.8912 E= 5.5e-049 -220 20 -140 104 -149 94 -1576 76 -1576 44 -1576 125 -1576 115 -116 68 -1576 -1576 -351 164 -336 176 -1576 11 -345 39 -1576 121 -206 62 -126 84 -1576 72 -1576 114 -328 81 -58 72 -192 -568 -510 153 -328 134 -210 54 -1576 12 -136 121 -236 4 -1576 125 -254 69 -1576 104 -1576 84 -58 79 -292 -21 -288 130 -1576 136 -23 21 -17 -183 -73 82 -128 81 -116 56 -113 38 -83 70 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTYTYTYTYTTTYTYWYT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 555 E= 5.5e-049 0.068468 0.212613 0.070270 0.648649 0.111712 0.354955 0.000000 0.533333 0.000000 0.252252 0.000000 0.747748 0.000000 0.412613 0.082883 0.504505 0.000000 0.000000 0.016216 0.983784 0.030631 0.628829 0.000000 0.340541 0.028829 0.243243 0.000000 0.727928 0.075676 0.284685 0.077477 0.562162 0.000000 0.306306 0.000000 0.693694 0.032432 0.326126 0.124324 0.517117 0.082883 0.003604 0.005405 0.908108 0.032432 0.468468 0.043243 0.455856 0.000000 0.201802 0.072072 0.726126 0.061261 0.190991 0.000000 0.747748 0.054054 0.299099 0.000000 0.646847 0.000000 0.331532 0.124324 0.544144 0.041441 0.160360 0.025225 0.772973 0.000000 0.477477 0.158559 0.363964 0.279279 0.052252 0.111712 0.556757 0.129730 0.324324 0.082883 0.463063 0.144144 0.241441 0.104505 0.509910 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTYTYTYTYTYTTTYTYWYT MEME-2 regular expression -------------------------------------------------------------------------------- [TC][TC][TC][TC]T[CT][TC][TC][TC][TC]T[CT][TC]T[TC][TC]T[CT][TA][TC][TC] -------------------------------------------------------------------------------- Time 229.91 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************