******************************************************************************** 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/AT5G64750_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/AT5G64750_peak_sequences.fasta -dna -oc out/AT5G64750 -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= 5822 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= 1216406 N= 5822 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.262 C 0.238 G 0.238 T 0.262 Background letter frequencies (from file dataset with add-one prior applied): A 0.263 C 0.237 G 0.237 T 0.263 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HHDCCGCCGCCRWHD MEME-1 width = 15 sites = 5810 llr = 47632 E-value = 1.1e-467 ******************************************************************************** -------------------------------------------------------------------------------- Motif HHDCCGCCGCCRWHD MEME-1 Description -------------------------------------------------------------------------------- Simplified A 22212::::135333 pos.-specific C 45158:aa:66:221 probability G 1132:a::a1:3112 matrix T 3232:::::312444 bits 2.1 ** 1.9 **** 1.7 **** 1.5 **** Relative 1.2 **** Entropy 1.0 ***** (11.8 bits) 0.8 ***** * 0.6 ******* 0.4 ******** 0.2 ** *********** 0.0 --------------- Multilevel CCTCCGCCGCCATTT consensus TTGT TAGAAA sequence AA CCG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDCCGCCGCCRWHD MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1134898 bayes= 9.52008 E= 1.1e-467 -40 59 -106 33 -17 98 -188 -16 -27 -93 42 37 -132 110 -59 -19 -40 167 -273 -427 -449 -1915 205 -491 -577 206 -459 -1915 -433 206 -1915 -1915 -567 -1915 207 -1057 -202 139 -190 -6 4 144 -1915 -159 91 -337 40 -63 8 -13 -208 77 17 -12 -120 54 8 -109 -3 52 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDCCGCCGCCRWHD MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 5810 E= 1.1e-467 0.198967 0.356799 0.113769 0.330465 0.233907 0.465921 0.064200 0.235972 0.218244 0.124269 0.317212 0.340275 0.105508 0.506713 0.157487 0.230293 0.198795 0.751807 0.035800 0.013597 0.011704 0.000000 0.979518 0.008778 0.004819 0.985370 0.009811 0.000000 0.013081 0.986919 0.000000 0.000000 0.005164 0.000000 0.994664 0.000172 0.064888 0.619966 0.063511 0.251635 0.270912 0.641652 0.000000 0.087435 0.495009 0.022892 0.312048 0.170052 0.277625 0.217212 0.055938 0.449225 0.295525 0.217384 0.103270 0.383821 0.277625 0.111360 0.232702 0.378313 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDCCGCCGCCRWHD MEME-1 regular expression -------------------------------------------------------------------------------- [CT][CTA][TGA][CT]CGCCG[CT][CA][AG][TAC][TAC][TAG] -------------------------------------------------------------------------------- Time 72.50 secs. ******************************************************************************** ******************************************************************************** MOTIF RRAGARRRAGARRAAGARRAR MEME-2 width = 21 sites = 2353 llr = 22669 E-value = 8.9e-123 ******************************************************************************** -------------------------------------------------------------------------------- Motif RRAGARRRAGARRAAGARRAR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 355274457195466384475 pos.-specific C :11112111::1:1::11::1 probability G 632723641914632714523 matrix T 112:11:11::1:11:11:11 bits 2.1 1.9 1.7 1.5 ** Relative 1.2 ** Entropy 1.0 * ** * * (13.9 bits) 0.8 * * ** * ** * 0.6 * ** * ** ** ** ** 0.4 * ** *********** ** 0.2 ********************* 0.0 --------------------- Multilevel GAAGAAGAAGAAGAAGAGGAA consensus AG A GAG GAG A AAGG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAGARRRAGARRAAGARRAR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1099966 bayes= 11.1513 E= 8.9e-123 36 -408 126 -170 78 -121 42 -104 103 -108 -27 -77 -25 -217 161 -727 144 -173 -56 -225 48 -54 47 -87 44 -216 132 -927 96 -201 59 -188 132 -199 -71 -91 -151 -912 189 -314 176 -306 -154 -1784 88 -111 57 -230 43 -912 145 -1784 121 -156 13 -232 130 -225 -46 -101 -1 -1784 162 -447 152 -123 -186 -177 47 -109 75 -106 51 -225 120 -308 147 -1784 -20 -200 79 -195 50 -81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAGARRRAGARRAAGARRAR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 2353 E= 8.9e-123 0.338292 0.014025 0.566511 0.081173 0.451764 0.102422 0.317892 0.127922 0.537612 0.111772 0.195920 0.154696 0.221419 0.052699 0.724182 0.001700 0.713132 0.071398 0.160221 0.055249 0.365916 0.162771 0.327667 0.143646 0.355716 0.053124 0.590735 0.000425 0.513387 0.058649 0.356566 0.071398 0.655759 0.059499 0.144496 0.140246 0.092648 0.000425 0.877178 0.029749 0.889928 0.028474 0.081598 0.000000 0.485763 0.110072 0.350616 0.053549 0.354016 0.000425 0.645559 0.000000 0.607310 0.080323 0.259669 0.052699 0.647259 0.049724 0.172121 0.130897 0.260518 0.000000 0.727582 0.011900 0.756906 0.100722 0.065448 0.076923 0.364216 0.111347 0.398640 0.125797 0.374841 0.049724 0.544411 0.031024 0.727582 0.000000 0.206545 0.065873 0.453464 0.061198 0.335742 0.149596 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif RRAGARRRAGARRAAGARRAR MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG]A[GA]A[AG][GA][AG]AGA[AG][GA][AG]A[GA]A[GA][GA][AG][AG] -------------------------------------------------------------------------------- Time 139.54 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************