******************************************************************************** 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/AT1G53170_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/AT1G53170_peak_sequences.fasta -dna -oc out/AT1G53170 -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= 7339 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= 1724281 N= 7339 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 0.263 C 0.237 G 0.237 T 0.263 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF HDYCGCCGCCRHHDH MEME-1 width = 15 sites = 7313 llr = 60066 E-value = 4.1e-384 ******************************************************************************** -------------------------------------------------------------------------------- Motif HDYCGCCGCCRHHDH MEME-1 Description -------------------------------------------------------------------------------- Simplified A 23121::::142332 pos.-specific C 4148:9a:79:2213 probability G 121:9::a1:51121 matrix T 343:1:::2:14443 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 CTCCGCCGCCGTTTT consensus TAT T ACAAC sequence AG ACGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDYCGCCGCCRHHDH MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 1621535 bayes= 9.81082 E= 4.1e-384 -23 91 -189 3 6 -96 -14 56 -96 87 -98 24 -61 172 -349 -330 -216 -1075 189 -208 -436 199 -298 -413 -409 206 -1948 -1948 -591 -1948 207 -1948 -293 152 -209 -18 -130 185 -1075 -286 49 -459 112 -129 -15 7 -173 75 8 2 -115 51 12 -122 -12 58 -18 37 -106 40 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDYCGCCGCCRHHDH MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 7313 E= 4.1e-384 0.223985 0.444004 0.063996 0.268016 0.275263 0.121838 0.214276 0.388623 0.135239 0.434158 0.120197 0.310406 0.172843 0.779297 0.021058 0.026802 0.058799 0.000137 0.878983 0.062081 0.012854 0.942158 0.029947 0.015042 0.015452 0.984548 0.000000 0.000000 0.004376 0.000000 0.995624 0.000000 0.034596 0.677014 0.055518 0.232873 0.106933 0.856557 0.000137 0.036374 0.369206 0.009845 0.513606 0.107343 0.237522 0.248598 0.071516 0.442363 0.278135 0.240531 0.106933 0.374402 0.285929 0.101326 0.218378 0.394366 0.233010 0.306030 0.113360 0.347600 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HDYCGCCGCCRHHDH MEME-1 regular expression -------------------------------------------------------------------------------- [CTA][TAG][CT]CGCCG[CT]C[GA][TCA][TAC][TAG][TCA] -------------------------------------------------------------------------------- Time 122.58 secs. ******************************************************************************** ******************************************************************************** MOTIF NRRARRHGRMRRAGRARRAGRARRAGA MEME-2 width = 27 sites = 3453 llr = 33720 E-value = 6.4e-138 ******************************************************************************** -------------------------------------------------------------------------------- Motif NRRARRHGRMRRAGRARRAGRARRAGA MEME-2 Description -------------------------------------------------------------------------------- Simplified A 344534424433626534626545826 pos.-specific C 2::1:12113:12::2:12::2::111 probability G 354253153266:84255174265:73 matrix T 21121222121:1::2112::1::1:1 bits 2.1 1.9 1.7 1.5 Relative 1.2 Entropy 1.0 * *** (14.1 bits) 0.8 * ** ** **** 0.6 ***** * ** **** 0.4 ** * * ***** ***** ***** 0.2 ***** ** ***************** 0.0 --------------------------- Multilevel AGAAGAAGAAGGAGAAGGAGAAGAAGA consensus GAG AGCAGCAACAG AA AGGAG G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NRRARRHGRMRRAGRARRAGRARRAGA MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 27 n= 1533467 bayes= 11.0895 E= 6.4e-138 30 -36 40 -55 50 -318 104 -119 74 -261 78 -119 90 -67 -30 -66 36 -317 104 -83 59 -105 49 -75 55 6 -94 -10 -9 -197 111 -53 72 -85 39 -108 47 26 -39 -63 31 -967 133 -175 38 -197 124 -279 127 -14 -389 -99 -37 -967 167 -259 112 -406 80 -666 84 -48 -27 -70 40 -282 121 -191 59 -186 98 -190 120 -63 -163 -66 -29 -349 160 -248 117 -1840 65 -277 94 -59 3 -144 56 -609 136 -1840 93 -651 107 -1840 162 -175 -1840 -111 -49 -184 161 -337 111 -137 16 -177 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NRRARRHGRMRRAGRARRAGRARRAGA MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 27 nsites= 3453 E= 6.4e-138 0.323487 0.185056 0.311903 0.179554 0.372719 0.026064 0.486244 0.114972 0.439328 0.038807 0.406313 0.115552 0.492326 0.148856 0.191717 0.167101 0.338546 0.026354 0.486823 0.148277 0.396177 0.114683 0.332175 0.156965 0.385462 0.246163 0.123371 0.245004 0.246742 0.060527 0.510860 0.181871 0.434405 0.131190 0.310165 0.124240 0.365190 0.284390 0.180133 0.170287 0.326962 0.000290 0.594555 0.078193 0.342890 0.060237 0.558934 0.037938 0.636258 0.215175 0.015928 0.132638 0.203881 0.000290 0.752100 0.043730 0.570518 0.014191 0.412685 0.002606 0.471184 0.169708 0.196641 0.162467 0.347234 0.033594 0.549377 0.069794 0.396467 0.065161 0.467709 0.070663 0.603823 0.152621 0.076745 0.166811 0.214886 0.021141 0.716768 0.047205 0.591080 0.000000 0.370403 0.038517 0.503910 0.157834 0.241529 0.096727 0.388068 0.003475 0.608456 0.000000 0.500145 0.002606 0.497249 0.000000 0.807703 0.070374 0.000000 0.121923 0.186794 0.066030 0.721691 0.025485 0.567043 0.091515 0.264408 0.077034 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif NRRARRHGRMRRAGRARRAGRARRAGA MEME-2 regular expression -------------------------------------------------------------------------------- [AG][GA][AG]A[GA][AG][ACT][GA][AG][AC][GA][GA][AC][GA][AG]A[GA][GA]A[GA][AG][AG][GA][AG]AG[AG] -------------------------------------------------------------------------------- Time 231.07 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************