******************************************************************************** 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/AT5G65130_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/AT5G65130_peak_sequences.fasta -dna -oc out/AT5G65130 -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= 4700 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= 1000432 N= 4700 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.263 C 0.237 G 0.237 T 0.263 Background letter frequencies (from file dataset with add-one prior applied): A 0.265 C 0.235 G 0.235 T 0.265 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HHDHCDCCRCCGMCR MEME-1 width = 15 sites = 4694 llr = 38958 E-value = 1.3e-509 ******************************************************************************** -------------------------------------------------------------------------------- Motif HHDHCDCCRCCGMCR MEME-1 Description -------------------------------------------------------------------------------- Simplified A 223223114:::4:4 pos.-specific C 34145168:aa:4a2 probability G 1121131:6::a::2 matrix T 3333232:::::2:2 bits 2.1 *** * 1.9 *** * 1.7 *** * 1.5 *** * Relative 1.3 * *** * Entropy 1.0 ***** * (12.0 bits) 0.8 ***** * 0.6 ***** * 0.4 ******** 0.2 * ** ********* 0.0 --------------- Multilevel CCTCCTCCGCCGCCA consensus TTATAGT A A G sequence AAG TA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDHCDCCRCCGMCR MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 934632 bayes= 9.46524 E= 1.3e-509 -22 57 -83 14 -20 67 -105 10 19 -70 5 22 -43 72 -84 11 -22 100 -157 -25 -5 -114 36 34 -148 123 -108 -13 -141 185 -291 -346 72 -1884 124 -486 -1884 209 -678 -770 -1884 209 -1884 -1884 -492 -1884 208 -1884 54 93 -404 -81 -589 208 -1884 -564 69 -31 -2 -81 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDHCDCCRCCGMCR MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 4694 E= 1.3e-509 0.227524 0.348743 0.132510 0.291223 0.230720 0.372603 0.113336 0.283340 0.303579 0.144440 0.243076 0.308905 0.197060 0.385599 0.131018 0.286323 0.227524 0.470175 0.078824 0.223477 0.256924 0.106732 0.301449 0.334896 0.095228 0.551129 0.110993 0.242650 0.099702 0.844908 0.031317 0.024073 0.437580 0.000000 0.553259 0.009161 0.000000 0.996591 0.002130 0.001278 0.000000 1.000000 0.000000 0.000000 0.008735 0.000000 0.991265 0.000000 0.385812 0.448232 0.014274 0.151683 0.004474 0.990200 0.000000 0.005326 0.427141 0.189391 0.232211 0.151257 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HHDHCDCCRCCGMCR MEME-1 regular expression -------------------------------------------------------------------------------- [CTA][CTA][TAG][CT][CAT][TGA][CT]C[GA]CCG[CA]C[AG] -------------------------------------------------------------------------------- Time 70.60 secs. ******************************************************************************** ******************************************************************************** MOTIF GRMGRAGRARRAGRMGRAGRR MEME-2 width = 21 sites = 1574 llr = 16297 E-value = 9.5e-118 ******************************************************************************** -------------------------------------------------------------------------------- Motif GRMGRAGRARRAGRMGRAGRR MEME-2 Description -------------------------------------------------------------------------------- Simplified A 255247155336244345254 pos.-specific C ::3::::12111:13::1::1 probability G 84176:84265:851761842 matrix T ::1::3::2112::2::2:12 bits 2.1 1.9 1.7 1.5 Relative 1.3 * * * * Entropy 1.0 * * * * ** * (14.9 bits) 0.8 * ***** * ** * 0.6 ** ***** ** ** ** 0.4 ** ***** ***** ** ** 0.2 ********************* 0.0 --------------------- Multilevel GAAGGAGAAGGAGGAGGAGAA consensus AGCAAT G AATAACAAT GG sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRMGRAGRARRAGRMGRAGRR MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 906432 bayes= 11.4765 E= 9.5e-118 -24 -1726 172 -612 85 -246 93 -300 81 17 -73 -106 -14 -1726 163 -300 48 -853 134 -298 133 -1726 -462 28 -99 -255 174 -273 104 -215 77 -1726 80 -27 -56 -53 12 -210 127 -157 36 -198 119 -200 124 -86 -853 -12 -22 -1726 172 -1726 62 -160 101 -260 71 13 -97 -48 17 -1726 158 -1726 66 -853 129 -554 99 -75 -102 -27 -47 -1726 178 -1726 105 -1726 67 -177 73 -132 9 -30 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRMGRAGRARRAGRMGRAGRR MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 1574 E= 9.5e-118 0.224269 0.000000 0.771919 0.003812 0.477764 0.042567 0.446633 0.033037 0.466328 0.264930 0.141677 0.127065 0.241423 0.000000 0.725540 0.033037 0.369759 0.000635 0.595934 0.033672 0.668361 0.000000 0.009530 0.322109 0.133418 0.040025 0.786531 0.040025 0.545743 0.052732 0.401525 0.000000 0.463151 0.194409 0.158831 0.183609 0.289072 0.054638 0.566709 0.089581 0.339898 0.059720 0.534307 0.066074 0.625159 0.129606 0.000635 0.244600 0.228081 0.000000 0.771919 0.000000 0.407243 0.077510 0.471410 0.043837 0.432656 0.256671 0.120076 0.190597 0.299238 0.000000 0.700762 0.000000 0.419314 0.000635 0.574333 0.005718 0.525413 0.139136 0.115629 0.219822 0.191868 0.000000 0.808132 0.000000 0.548285 0.000000 0.374206 0.077510 0.440280 0.094028 0.249682 0.216010 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif GRMGRAGRARRAGRMGRAGRR MEME-2 regular expression -------------------------------------------------------------------------------- [GA][AG][AC][GA][GA][AT]G[AG]A[GA][GA][AT][GA][GA][AC][GA][GA][AT]G[AG][AGT] -------------------------------------------------------------------------------- Time 135.93 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************