******************************************************************************** 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/AT3G04070_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/AT3G04070_peak_sequences.fasta -dna -oc out/AT3G04070 -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= 4460 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= 833591 N= 4460 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.324 C 0.176 G 0.176 T 0.324 Background letter frequencies (from file dataset with add-one prior applied): A 0.326 C 0.174 G 0.174 T 0.326 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF AAGWKACGTGT MEME-1 width = 11 sites = 4435 llr = 28785 E-value = 6.6e-141 ******************************************************************************** -------------------------------------------------------------------------------- Motif AAGWKACGTGT MEME-1 Description -------------------------------------------------------------------------------- Simplified A 462416:::33 pos.-specific C 211::29::11 probability G 236:42:9:71 matrix T 211651:1a:5 bits 2.5 2.3 * 2.0 ** 1.8 ** Relative 1.5 *** Entropy 1.3 *** (9.4 bits) 1.0 **** 0.8 * **** 0.5 *** **** 0.3 ********* 0.0 ----------- Multilevel AAGTTACGTGT consensus TGAAG AA sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGWKACGTGT MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 788991 bayes= 9.24676 E= 6.6e-141 44 7 -11 -62 82 -141 62 -183 -49 -85 177 -212 41 -535 -959 79 -155 -270 115 54 78 -16 4 -162 -333 242 -1876 -340 -1876 -1876 244 -259 -1876 -660 -1876 162 -36 -123 190 -399 -34 -56 -76 68 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGWKACGTGT MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 4435 E= 6.6e-141 0.442616 0.183766 0.162120 0.211499 0.573844 0.065614 0.268997 0.091545 0.232469 0.096956 0.595716 0.074859 0.432244 0.004284 0.000225 0.563247 0.110936 0.026832 0.388501 0.473732 0.558286 0.156483 0.179481 0.105750 0.032469 0.936640 0.000000 0.030891 0.000000 0.000000 0.945885 0.054115 0.000000 0.001804 0.000000 0.998196 0.254115 0.074408 0.650958 0.020519 0.257497 0.118602 0.102818 0.521082 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif AAGWKACGTGT MEME-1 regular expression -------------------------------------------------------------------------------- [AT][AG][GA][TA][TG]ACGT[GA][TA] -------------------------------------------------------------------------------- Time 73.33 secs. ******************************************************************************** ******************************************************************************** MOTIF HTYTYYTTYTTYTTYTTYTTY MEME-2 width = 21 sites = 784 llr = 8700 E-value = 1.3e-068 ******************************************************************************** -------------------------------------------------------------------------------- Motif HTYTYYTTYTTYTTYTTYTTY MEME-2 Description -------------------------------------------------------------------------------- Simplified A 22:::11::11:::::::::: pos.-specific C 3:6:33225134315124325 probability G 2:::111::1::1::1::::1 matrix T 484a65785876684876783 bits 2.5 2.3 2.0 1.8 Relative 1.5 * Entropy 1.3 * (16.0 bits) 1.0 ** * * * 0.8 **** ***** ******* 0.5 **** *************** 0.3 ******************** 0.0 --------------------- Multilevel TTCTTTTTCTTTTTCTTTTTC consensus C T CCC T CCC T CCC T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTYYTTYTTYTTYTTYTTY MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 744391 bayes= 12.1835 E= 1.3e-068 -77 73 -19 17 -109 -1626 -234 132 -1626 171 -214 26 -1626 -1626 -205 156 -1626 85 -40 77 -173 67 -99 72 -267 30 -134 103 -1626 -12 -1626 137 -519 144 -197 54 -264 -50 -170 124 -247 67 -393 100 -519 122 -1626 84 -291 52 -154 99 -287 -57 -245 131 -287 155 -205 30 -799 -47 -126 130 -483 47 -293 115 -483 116 -234 80 -309 63 -1626 109 -1626 -12 -1626 137 -309 150 -50 8 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTYYTTYTTYTTYTTYTTY MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 784 E= 1.3e-068 0.191327 0.289541 0.153061 0.366071 0.153061 0.000000 0.034439 0.812500 0.000000 0.570153 0.039541 0.390306 0.000000 0.000000 0.042092 0.957908 0.000000 0.313776 0.132653 0.553571 0.098214 0.276786 0.088010 0.536990 0.051020 0.214286 0.068878 0.665816 0.000000 0.160714 0.000000 0.839286 0.008929 0.474490 0.044643 0.471939 0.052296 0.123724 0.053571 0.770408 0.058673 0.276786 0.011480 0.653061 0.008929 0.406888 0.000000 0.584184 0.043367 0.250000 0.059949 0.646684 0.044643 0.117347 0.031888 0.806122 0.044643 0.511480 0.042092 0.401786 0.001276 0.126276 0.072704 0.799745 0.011480 0.241071 0.022959 0.724490 0.011480 0.389031 0.034439 0.565051 0.038265 0.269133 0.000000 0.692602 0.000000 0.160714 0.000000 0.839286 0.038265 0.494898 0.123724 0.343112 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif HTYTYYTTYTTYTTYTTYTTY MEME-2 regular expression -------------------------------------------------------------------------------- [TC]T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[CT]T[TC][TC][TC]T[CT] -------------------------------------------------------------------------------- Time 135.74 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************