******************************************************************************** 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/AT1G32150_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/AT1G32150_peak_sequences.fasta -dna -oc out/AT1G32150 -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= 3406 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= 750064 N= 3406 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.3 C 0.2 G 0.2 T 0.3 Background letter frequencies (from file dataset with add-one prior applied): A 0.301 C 0.199 G 0.199 T 0.301 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF TGCCACGTSDNM MEME-1 width = 12 sites = 3368 llr = 32412 E-value = 8.2e-687 ******************************************************************************** -------------------------------------------------------------------------------- Motif TGCCACGTSDNM MEME-1 Description -------------------------------------------------------------------------------- Simplified A 1:3:a:::1423 pos.-specific C 2:7a:a::4:35 probability G 18::::9:5331 matrix T 62:::::a:322 bits 2.3 * 2.1 * * 1.9 * ** 1.6 ***** Relative 1.4 * ***** Entropy 1.2 ******* (13.9 bits) 0.9 ******** 0.7 ******** 0.5 ******** 0.2 ********** * 0.0 ------------ Multilevel TGCCACGTGACC consensus C A CTGA sequence GTT A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCACGTSDNM MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 712598 bayes= 9.93982 E= 8.2e-687 -125 16 -104 88 -481 -514 198 -59 2 180 -1836 -740 -1836 233 -1836 -1836 173 -1836 -1836 -1836 -608 226 -414 -339 -267 -300 222 -718 -1836 -622 -493 172 -158 85 141 -453 36 -410 40 17 -49 61 36 -40 -24 124 -187 -46 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCACGTSDNM MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 3368 E= 8.2e-687 0.126781 0.221793 0.096793 0.554632 0.010689 0.005641 0.784145 0.199525 0.306116 0.692102 0.000000 0.001781 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.004454 0.955463 0.011283 0.028800 0.047209 0.024941 0.925772 0.002078 0.000000 0.002672 0.006532 0.990796 0.100950 0.358373 0.527613 0.013064 0.387173 0.011580 0.262470 0.338777 0.214074 0.302850 0.255344 0.227732 0.254454 0.471793 0.054632 0.219121 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TGCCACGTSDNM MEME-1 regular expression -------------------------------------------------------------------------------- [TC]G[CA]CACGT[GC][ATG][CGTA][CAT] -------------------------------------------------------------------------------- Time 119.18 secs. ******************************************************************************** ******************************************************************************** MOTIF TYTTYTTYTTYYTYT MEME-2 width = 15 sites = 1075 llr = 10417 E-value = 3.9e-083 ******************************************************************************** -------------------------------------------------------------------------------- Motif TYTTYTTYTTYYTYT MEME-2 Description -------------------------------------------------------------------------------- Simplified A :::::::::::1::: pos.-specific C 161343:61343:53 probability G :::::11:::1:::: matrix T 849766939755957 bits 2.3 2.1 1.9 1.6 Relative 1.4 Entropy 1.2 ** * * (14.0 bits) 0.9 ***** **** ** 0.7 *********** *** 0.5 *************** 0.2 *************** 0.0 --------------- Multilevel TCTTTTTCTTTTTTT consensus T CCC T CCC CC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYYTYT MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 702380 bayes= 11.5898 E= 3.9e-083 -464 -70 -304 148 -601 165 -1671 30 -1671 -83 -322 153 -1671 57 -493 121 -1671 112 -416 89 -1671 33 -82 108 -321 -232 -151 151 -1671 165 -222 13 -325 -114 -1671 155 -1671 50 -1671 125 -1671 100 -183 86 -207 79 -213 84 -264 -304 -279 158 -1671 129 -288 70 -275 44 -257 111 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYYTYT MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 1075 E= 3.9e-083 0.012093 0.122791 0.024186 0.840930 0.004651 0.626047 0.000000 0.369302 0.000000 0.111628 0.021395 0.866977 0.000000 0.295814 0.006512 0.697674 0.000000 0.432558 0.011163 0.556279 0.000000 0.250233 0.112558 0.637209 0.032558 0.040000 0.069767 0.857674 0.000000 0.626977 0.042791 0.330233 0.031628 0.090233 0.000000 0.878140 0.000000 0.281860 0.000000 0.718140 0.000000 0.397209 0.055814 0.546977 0.071628 0.345116 0.045581 0.537674 0.048372 0.024186 0.028837 0.898605 0.000000 0.485581 0.026977 0.487442 0.044651 0.270698 0.033488 0.651163 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif TYTTYTTYTTYYTYT MEME-2 regular expression -------------------------------------------------------------------------------- T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[TC][TC] -------------------------------------------------------------------------------- Time 226.90 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************