******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 3.0 (Release date: 2004/07/26 08:17:15) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.sdsc.edu. This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.sdsc.edu. ******************************************************************************** ******************************************************************************** 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 ******************************************************************************** DATAFILE= all_X_D.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ CfDhoxD1 1.0000 501 CfDhoxD3 1.0000 501 CfDhoxD4 1.0000 501 CfDhoxD8 1.0000 501 CfDhoxD9 1.0000 501 CfDhoxD10 1.0000 501 CfDhoxD11 1.0000 501 CfDhoxD12 1.0000 501 CfDhoxD13 1.0000 501 HsDhoxD1 1.0000 501 HsDhoxD3 1.0000 501 HsDhoxD4 1.0000 501 HsDhoxD8 1.0000 501 HsDhoxD9 1.0000 501 HsDhoxD10 1.0000 501 HsDhoxD11 1.0000 501 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme all_X_D.fa -dna -mod zoops -minw 10 -maxw 10 -wg 11 -ws 1 -nmotifs 10 -evt 1e+07 -revcomp -maxiter 50 -distance 0.001 -prior dirichlet -b 0.01 -maxsize 1000000 model: mod= zoops nmotifs= 10 evt= 1e+07 object function= E-value of product of p-values width: minw= 10 maxw= 10 minic= 0.00 width: wg= 11 ws= 1 endgaps= yes nsites: minsites= 2 maxsites= 16 wnsites= 0.8 theta: prob= 1 spmap= uni spfuzz= 0.5 em: prior= dirichlet b= 0.01 maxiter= 50 distance= 0.001 data: n= 8016 N= 16 strands: + - sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.196 C 0.304 G 0.304 T 0.196 Background letter frequencies (from dataset with add-one prior applied): A 0.196 C 0.304 G 0.304 T 0.196 ******************************************************************************** ******************************************************************************** MOTIF 1 width = 10 sites = 11 llr = 126 E-value = 7.8e-002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 4:::::::1: pos.-specific C ::11:::922 probability G :12:::2::: matrix T 6979aa8178 bits 2.3 ** 2.1 ** 1.9 * *** 1.6 * **** * Information 1.4 ** ***** * content 1.2 ********** (16.5 bits) 0.9 ********** 0.7 ********** 0.5 ********** 0.2 ********** 0.0 ---------- Multilevel TTTTTTTCTT consensus A sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsDhoxD8 + 6 1.31e-07 GGTGT TTTTTTTCTT TTCCCTCCAG HsDhoxD9 + 308 7.53e-07 ATGTTGATGA TTTTTTTTTT AATCACAGCA HsDhoxD4 - 449 1.16e-06 TCGTGTTGTC TTTTTTTCTC CTTCCATAGG CfDhoxD4 - 449 1.16e-06 TCGTGTTGTC TTTTTTTCTC CTTCCATAGG CfDhoxD13 + 430 1.29e-06 CCTGGTCTAA TTTTTTTCAT GCTGTTTTTT HsDhoxD11 + 396 2.39e-06 CCCGGTGGGG ATTTTTGCTT AGTTGATCCT CfDhoxD11 + 396 2.39e-06 CCCGGTGGGG ATTTTTGCTT AGTTGATCCT CfDhoxD3 - 162 2.93e-06 CAGACACTAT TTTCTTTCTT CAAGATTGTC HsDhoxD10 + 437 6.96e-06 TACACGGGGA ATGTTTTCCT AGAGATGTCA CfDhoxD10 + 437 6.96e-06 TACACGGGGA ATGTTTTCCT AGAGATGTCA HsDhoxD3 + 400 1.76e-05 TGGGGCCTCT TGCTTTTCTT CTGACAGGTC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsDhoxD8 1.3e-07 5_[+1]_486 HsDhoxD9 7.5e-07 307_[+1]_184 HsDhoxD4 1.2e-06 448_[-1]_43 CfDhoxD4 1.2e-06 448_[-1]_43 CfDhoxD13 1.3e-06 429_[+1]_62 HsDhoxD11 2.4e-06 395_[+1]_96 CfDhoxD11 2.4e-06 395_[+1]_96 CfDhoxD3 2.9e-06 161_[-1]_330 HsDhoxD10 7e-06 436_[+1]_55 CfDhoxD10 7e-06 436_[+1]_55 HsDhoxD3 1.8e-05 399_[+1]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=10 seqs=11 HsDhoxD8 ( 6) TTTTTTTCTT 1 HsDhoxD9 ( 308) TTTTTTTTTT 1 HsDhoxD4 ( 449) TTTTTTTCTC 1 CfDhoxD4 ( 449) TTTTTTTCTC 1 CfDhoxD13 ( 430) TTTTTTTCAT 1 HsDhoxD11 ( 396) ATTTTTGCTT 1 CfDhoxD11 ( 396) ATTTTTGCTT 1 CfDhoxD3 ( 162) TTTCTTTCTT 1 HsDhoxD10 ( 437) ATGTTTTCCT 1 CfDhoxD10 ( 437) ATGTTTTCCT 1 HsDhoxD3 ( 400) TGCTTTTCTT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 7872 bayes= 9.8366 E= 7.8e-002 89 -1010 -1010 170 -1010 -1010 -174 221 -1010 -174 -74 189 -1010 -174 -1010 221 -1010 -1010 -1010 235 -1010 -1010 -1010 235 -1010 -1010 -74 206 -1010 158 -1010 -111 -111 -74 -1010 189 -1010 -74 -1010 206 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 11 E= 7.8e-002 0.363636 0.000000 0.000000 0.636364 0.000000 0.000000 0.090909 0.909091 0.000000 0.090909 0.181818 0.727273 0.000000 0.090909 0.000000 0.909091 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.181818 0.818182 0.000000 0.909091 0.000000 0.090909 0.090909 0.181818 0.000000 0.727273 0.000000 0.181818 0.000000 0.818182 -------------------------------------------------------------------------------- Time 2.77 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 width = 10 sites = 15 llr = 140 E-value = 2.3e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 11:1:::::: pos.-specific C :2:5:a1::: probability G 97a3a::a9a matrix T 1::1::9:1: bits 2.3 2.1 1.9 1.6 * **** * Information 1.4 * ****** content 1.2 * * ****** (13.5 bits) 0.9 * * ****** 0.7 * * ****** 0.5 *** ****** 0.2 *** ****** 0.0 ---------- Multilevel GGGCGCTGGG consensus C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Strand Start P-value Site ------------- ------ ----- --------- ---------- HsDhoxD1 + 147 4.32e-06 CGGGGCTCGG GGGCGCTGGG CGGCGGCCCT HsDhoxD8 + 218 8.64e-06 GGCGGCGCGC GGGGGCTGGG CGAGGCCCCG CfDhoxD8 + 40 8.64e-06 CGGCGAGCGC GGGGGCTGGG CGAGGCCCCG HsDhoxD4 + 231 1.42e-05 GAGGGGAATG GGGTGCTGGG GACTGGAACT CfDhoxD4 + 230 1.42e-05 CCAGGAGCGA GGGTGCTGGG GATTAGAGAA HsDhoxD10 + 241 1.70e-05 GGGCGGCGGA GAGCGCTGGG CCGGTTGTCT HsDhoxD11 - 246 2.13e-05 GCCGAGACGC GCGCGCTGGG GGCGGATCGG CfDhoxD11 - 244 2.13e-05 CGAGACGCGC GCGCGCTGGG GGCGGACCGG CfDhoxD1 + 9 2.13e-05 CCTCCCGT GCGCGCTGGG GCGGCCGGCG HsDhoxD3 - 440 3.20e-05 TGAATCCTGA GAGAGCTGGG CCGGCCCCCA HsDhoxD9 - 173 4.32e-05 CATCCAGAGG AGGCGCTGGG GACTATTTGT CfDhoxD10 - 103 5.27e-05 AGGGAAGCCG GGGCGCCGGG GCGCCAGCGC CfDhoxD13 - 393 6.11e-05 GAGCACCACT GGGGGCTGTG TATGTACGTT CfDhoxD3 - 440 6.77e-05 CGAATCCTGA GGGGGCCGGG GTAGCCCCAG CfDhoxD12 - 222 7.49e-05 GCTCAGCTTC TGGAGCTGGG GACATTGGGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- HsDhoxD1 4.3e-06 146_[+2]_345 HsDhoxD8 8.6e-06 217_[+2]_274 CfDhoxD8 8.6e-06 39_[+2]_452 HsDhoxD4 1.4e-05 230_[+2]_261 CfDhoxD4 1.4e-05 229_[+2]_262 HsDhoxD10 1.7e-05 240_[+2]_251 HsDhoxD11 2.1e-05 245_[-2]_246 CfDhoxD11 2.1e-05 243_[-2]_248 CfDhoxD1 2.1e-05 8_[+2]_483 HsDhoxD3 3.2e-05 439_[-2]_52 HsDhoxD9 4.3e-05 172_[-2]_319 CfDhoxD10 5.3e-05 102_[-2]_389 CfDhoxD13 6.1e-05 392_[-2]_99 CfDhoxD3 6.8e-05 439_[-2]_52 CfDhoxD12 7.5e-05 221_[-2]_270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=10 seqs=15 HsDhoxD1 ( 147) GGGCGCTGGG 1 HsDhoxD8 ( 218) GGGGGCTGGG 1 CfDhoxD8 ( 40) GGGGGCTGGG 1 HsDhoxD4 ( 231) GGGTGCTGGG 1 CfDhoxD4 ( 230) GGGTGCTGGG 1 HsDhoxD10 ( 241) GAGCGCTGGG 1 HsDhoxD11 ( 246) GCGCGCTGGG 1 CfDhoxD11 ( 244) GCGCGCTGGG 1 CfDhoxD1 ( 9) GCGCGCTGGG 1 HsDhoxD3 ( 440) GAGAGCTGGG 1 HsDhoxD9 ( 173) AGGCGCTGGG 1 CfDhoxD10 ( 103) GGGCGCCGGG 1 CfDhoxD13 ( 393) GGGGGCTGTG 1 CfDhoxD3 ( 440) GGGGGCCGGG 1 CfDhoxD12 ( 222) TGGAGCTGGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 10 n= 7872 bayes= 8.95776 E= 2.3e+003 -156 -1055 151 -156 -56 -60 113 -1055 -1055 -1055 172 -1055 -56 62 -19 -56 -1055 -1055 172 -1055 -1055 172 -1055 -1055 -1055 -119 -1055 214 -1055 -1055 172 -1055 -1055 -1055 162 -156 -1055 -1055 172 -1055 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 10 nsites= 15 E= 2.3e+003 0.066667 0.000000 0.866667 0.066667 0.133333 0.200000 0.666667 0.000000 0.000000 0.000000 1.000000 0.000000 0.133333 0.466667 0.266667 0.133333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.133333 0.000000 0.866667 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.933333 0.066667 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- Time 6.41 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- CfDhoxD1 8.57e-02 8_[+2(2.13e-05)]_483 CfDhoxD3 1.78e-03 161_[-1(2.93e-06)]_268_[-2(6.77e-05)]_52 CfDhoxD4 1.91e-04 229_[+2(1.42e-05)]_209_[-1(1.16e-06)]_43 CfDhoxD8 4.89e-02 39_[+2(8.64e-06)]_452 CfDhoxD9 1.00e-00 501 CfDhoxD10 3.09e-03 102_[-2(5.27e-05)]_324_[+1(6.96e-06)]_55 CfDhoxD11 5.33e-04 243_[-2(2.13e-05)]_142_[+1(2.39e-06)]_96 CfDhoxD12 5.37e-02 221_[-2(7.49e-05)]_270 CfDhoxD13 7.78e-04 75_[-1(4.69e-05)]_23_[+1(3.30e-05)]_234_[+1(1.19e-05)]_30_[-2(6.11e-05)]_27_[+1(1.29e-06)]_2_[+1(4.07e-05)]_50 HsDhoxD1 4.91e-03 146_[+2(4.32e-06)]_345 HsDhoxD3 4.56e-03 399_[+1(1.76e-05)]_30_[-2(3.20e-05)]_52 HsDhoxD4 1.91e-04 230_[+2(1.42e-05)]_208_[-1(1.16e-06)]_43 HsDhoxD8 1.61e-05 5_[+1(1.31e-07)]_59_[+1(7.35e-05)]_133_[+2(8.64e-06)]_274 HsDhoxD9 3.51e-04 172_[-2(4.32e-05)]_125_[+1(7.53e-07)]_184 HsDhoxD10 1.14e-03 240_[+2(1.70e-05)]_186_[+1(6.96e-06)]_55 HsDhoxD11 5.33e-04 245_[-2(2.13e-05)]_140_[+1(2.39e-06)]_96 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because motif E-value > 1.00e+07. ******************************************************************************** CPU: hotchocolate.bioinf.uni-leipzig.de ********************************************************************************