******************************************************************************** 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/AT5G47390_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/AT5G47390_peak_sequences.fasta -dna -oc out/AT5G47390 -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= 7885 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= 2087990 N= 7885 sample: seed= 0 hsfrac= 0 searchsize= 100000 norand= no csites= 1000 Letter frequencies in dataset: A 0.352 C 0.148 G 0.148 T 0.352 Background letter frequencies (from file dataset with add-one prior applied): A 0.353 C 0.147 G 0.147 T 0.353 Background model order: 0 ******************************************************************************** ******************************************************************************** MOTIF YHTTATCCAWW MEME-1 width = 11 sites = 7873 llr = 58088 E-value = 9.3e-157 ******************************************************************************** -------------------------------------------------------------------------------- Motif YHTTATCCAWW MEME-1 Description -------------------------------------------------------------------------------- Simplified A 2211a:::746 pos.-specific C 441:::a8:2: probability G 11::::::11: matrix T 4389:a:2234 bits 2.8 * 2.5 * 2.2 * 1.9 * Relative 1.7 ** Entropy 1.4 **** (10.6 bits) 1.1 **** 0.8 ****** 0.6 ******* 0.3 ********* * 0.0 ----------- Multilevel CCTTATCCAAA consensus TT T TT sequence A C -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHTTATCCAWW MEME-1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 11 n= 2009140 bayes= 10.2253 E= 9.3e-157 -117 140 -99 10 -71 145 -23 -46 -153 -98 -1959 119 -197 -331 -566 134 150 -1959 -1959 -1959 -1959 -1959 -1959 150 -1959 276 -1959 -1959 -1959 242 -1959 -74 100 -321 -54 -101 24 45 -137 -12 70 -257 -393 16 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHTTATCCAWW MEME-1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 11 nsites= 7873 E= 9.3e-157 0.156484 0.390194 0.074305 0.379017 0.215420 0.402007 0.125619 0.256954 0.122444 0.074559 0.000000 0.802998 0.090182 0.014861 0.002921 0.892036 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.789153 0.000000 0.210847 0.707481 0.015877 0.101105 0.175537 0.417757 0.200813 0.057030 0.324400 0.572082 0.024768 0.009653 0.393497 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif YHTTATCCAWW MEME-1 regular expression -------------------------------------------------------------------------------- [CT][CTA]TTATC[CT]A[ATC][AT] -------------------------------------------------------------------------------- Time 81.18 secs. ******************************************************************************** ******************************************************************************** MOTIF WTBGGTTYGGWTTBGGTTYKK MEME-2 width = 21 sites = 257 llr = 3334 E-value = 3.9e-011 ******************************************************************************** -------------------------------------------------------------------------------- Motif WTBGGTTYGGWTTBGGTTYKK MEME-2 Description -------------------------------------------------------------------------------- Simplified A 321:22::2:4::1:22:1:2 pos.-specific C 124211:411::33:::15:: probability G ::3661::592::3a5::165 matrix T 663217962:4a73:289343 bits 2.8 * 2.5 * 2.2 * * 1.9 * * Relative 1.7 * * Entropy 1.4 * * * * (18.7 bits) 1.1 * ** * * * * * 0.8 ** ** * ** ** * * 0.6 **** **** ** ******* 0.3 ********************* 0.0 --------------------- Multilevel TTCGGTTTGGTTTTGGTTCGG consensus A G CT A CC T TTT sequence T G A A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTBGGTTYGGWTTBGGTTYKK MEME-2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 1930290 bayes= 15.1095 E= 3.9e-011 -22 -60 -1465 77 -104 34 -1465 86 -204 130 100 -46 -650 43 206 -95 -83 -20 194 -169 -108 -154 -44 93 -292 -1465 -244 139 -1465 159 -1465 66 -95 -60 171 -57 -550 -116 265 -650 11 -1465 25 33 -1465 -1465 -524 150 -1465 93 -266 98 -169 97 82 -4 -650 -524 275 -1465 -67 -1465 185 -52 -98 -224 -524 116 -292 -116 -1465 133 -241 169 -39 -3 -650 -1465 203 16 -77 -1465 173 -22 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTBGGTTYGGWTTBGGTTYKK MEME-2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 257 E= 3.9e-011 0.303502 0.097276 0.000000 0.599222 0.171206 0.186770 0.000000 0.642023 0.085603 0.361868 0.295720 0.256809 0.003891 0.198444 0.614786 0.182879 0.198444 0.128405 0.564202 0.108949 0.167315 0.050584 0.108949 0.673152 0.046693 0.000000 0.027237 0.926070 0.000000 0.443580 0.000000 0.556420 0.182879 0.097276 0.482490 0.237354 0.007782 0.066148 0.922179 0.003891 0.381323 0.000000 0.175097 0.443580 0.000000 0.000000 0.003891 0.996109 0.000000 0.280156 0.023346 0.696498 0.108949 0.287938 0.260700 0.342412 0.003891 0.003891 0.992218 0.000000 0.221790 0.000000 0.533074 0.245136 0.178988 0.031128 0.003891 0.785992 0.046693 0.066148 0.000000 0.887160 0.066148 0.474708 0.112840 0.346304 0.003891 0.000000 0.603113 0.392996 0.206226 0.000000 0.490272 0.303502 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif WTBGGTTYGGWTTBGGTTYKK MEME-2 regular expression -------------------------------------------------------------------------------- [TA]T[CGT]GGTT[TC][GT]G[TA]T[TC][TCG]G[GTA]TT[CT][GT][GTA] -------------------------------------------------------------------------------- Time 153.24 secs. ******************************************************************************** ******************************************************************************** Stopped because requested number of motifs (2) found. ******************************************************************************** CPU: nid004083 ********************************************************************************