******************************************************************************** MEME - Motif discovery tool ******************************************************************************** MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000) For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net. 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.nbcr.net. ******************************************************************************** ******************************************************************************** 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= motifs/185/185.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 37858 1.0000 500 48173 1.0000 500 15063 1.0000 500 15214 1.0000 500 48755 1.0000 500 55069 1.0000 500 23811 1.0000 500 16698 1.0000 500 54169 1.0000 500 18808 1.0000 500 33631 1.0000 500 39325 1.0000 500 32160 1.0000 500 50065 1.0000 500 48042 1.0000 500 49812 1.0000 500 ******************************************************************************** ******************************************************************************** COMMAND LINE SUMMARY ******************************************************************************** This information can also be useful in the event you wish to report a problem with the MEME software. command: meme motifs/185/185.seqs.fa -oc motifs/185 -dna -minw 12 -maxw 21 -nmotifs 3 -maxsize 500000 model: mod= zoops nmotifs= 3 evt= inf object function= E-value of product of p-values width: minw= 12 maxw= 21 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 global: substring= yes branching= no wbranch= no em: prior= dirichlet b= 0.01 maxiter= 50 distance= 1e-05 data: n= 8000 N= 16 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.252 C 0.248 G 0.221 T 0.279 Background letter frequencies (from dataset with add-one prior applied): A 0.252 C 0.248 G 0.221 T 0.279 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 9 llr = 110 E-value = 3.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::a:4:::aa: pos.-specific C 714:9:1:4::: probability G 3:::::9:1::: matrix T :96:16:a4::a bits 2.2 2.0 * ** 1.7 * ** *** 1.5 ** ** *** Relative 1.3 * ** ** *** Entropy 1.1 ** ** ** *** (17.7 bits) 0.9 ******** *** 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel CTTACTGTCAAT consensus G C A T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 54169 187 3.57e-07 CTGTGACGTC CTTACTGTTAAT CCTTTGACCT 15214 287 3.57e-07 CTGTTTTACT CTTACTGTTAAT TCCGAAGACG 37858 194 3.57e-07 AACGGCTTCC CTTACTGTTAAT GTTTACAATT 32160 352 6.14e-07 CCAAATCAAT CTCACAGTCAAT AAATCTACCA 16698 92 1.01e-06 ACGTCTTACA GTTACTGTTAAT TGCTAGCGTC 48173 276 1.24e-06 TTGTGTCAGA GTCACAGTCAAT TGATAGCTAC 55069 295 3.87e-06 CGGACTCTTT CTCATAGTCAAT CACAGTCACA 15063 203 5.32e-06 CCCTAGCGGT GTCACTCTCAAT GCCGTCGGTA 33631 324 6.20e-06 ACTGCCTTTC CCTACAGTGAAT ACCTCTGCTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 54169 3.6e-07 186_[+1]_302 15214 3.6e-07 286_[+1]_202 37858 3.6e-07 193_[+1]_295 32160 6.1e-07 351_[+1]_137 16698 1e-06 91_[+1]_397 48173 1.2e-06 275_[+1]_213 55069 3.9e-06 294_[+1]_194 15063 5.3e-06 202_[+1]_286 33631 6.2e-06 323_[+1]_165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=9 54169 ( 187) CTTACTGTTAAT 1 15214 ( 287) CTTACTGTTAAT 1 37858 ( 194) CTTACTGTTAAT 1 32160 ( 352) CTCACAGTCAAT 1 16698 ( 92) GTTACTGTTAAT 1 48173 ( 276) GTCACAGTCAAT 1 55069 ( 295) CTCATAGTCAAT 1 15063 ( 203) GTCACTCTCAAT 1 33631 ( 324) CCTACAGTGAAT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 10.6108 E= 3.1e-001 -982 142 59 -982 -982 -116 -982 167 -982 84 -982 99 199 -982 -982 -982 -982 184 -982 -133 82 -982 -982 99 -982 -116 201 -982 -982 -982 -982 184 -982 84 -99 67 199 -982 -982 -982 199 -982 -982 -982 -982 -982 -982 184 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 9 E= 3.1e-001 0.000000 0.666667 0.333333 0.000000 0.000000 0.111111 0.000000 0.888889 0.000000 0.444444 0.000000 0.555556 1.000000 0.000000 0.000000 0.000000 0.000000 0.888889 0.000000 0.111111 0.444444 0.000000 0.000000 0.555556 0.000000 0.111111 0.888889 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.444444 0.111111 0.444444 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CG]T[TC]AC[TA]GT[CT]AAT -------------------------------------------------------------------------------- Time 1.98 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 7 llr = 125 E-value = 3.0e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :4:63:7:a:::6:113:1:: pos.-specific C 74::67:6:::6:13477::a probability G :17::314:a:4494::39:: matrix T 3:341:1:::a:::14:::a: bits 2.2 * 2.0 ** * 1.7 *** ** 1.5 *** * *** Relative 1.3 * *** * *** Entropy 1.1 * * * ******* ***** (25.8 bits) 0.9 * ** ********* ***** 0.7 ************** ***** 0.4 ************** ****** 0.2 ********************* 0.0 --------------------- Multilevel CAGACCACAGTCAGGCCCGTC consensus TCTTAG G GG CTAG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 49812 427 1.20e-10 TGTGTGTGAC CATTCCACAGTGAGGTCCGTC CTGTTTGGTG 48042 310 1.20e-10 TGTGTGTAAC CATTCCACAGTGAGGTCCGTC CTGTTTGGTG 48755 167 3.92e-10 GCGTACGACG CCGAACAGAGTCGGATCCGTC TACATTCCCG 39325 128 4.62e-09 ACTGCCAGTG TCGTTCACAGTCAGCCCGGTC CCTGTTTCAT 54169 329 7.52e-09 TAAAGTCGTA CAGACGACAGTCACGCCCATC GCTCTCAATA 23811 3 2.10e-08 AG TCGAACGGAGTCGGCAACGTC TATTTTGAGT 32160 121 3.74e-08 TTGATGGTCC CGGACGTGAGTGGGTCAGGTC CGCTCTGGAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49812 1.2e-10 426_[+2]_53 48042 1.2e-10 309_[+2]_170 48755 3.9e-10 166_[+2]_313 39325 4.6e-09 127_[+2]_352 54169 7.5e-09 328_[+2]_151 23811 2.1e-08 2_[+2]_477 32160 3.7e-08 120_[+2]_359 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=7 49812 ( 427) CATTCCACAGTGAGGTCCGTC 1 48042 ( 310) CATTCCACAGTGAGGTCCGTC 1 48755 ( 167) CCGAACAGAGTCGGATCCGTC 1 39325 ( 128) TCGTTCACAGTCAGCCCGGTC 1 54169 ( 329) CAGACGACAGTCACGCCCATC 1 23811 ( 3) TCGAACGGAGTCGGCAACGTC 1 32160 ( 121) CGGACGTGAGTGGGTCAGGTC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 9.94195 E= 3.0e-001 -945 152 -945 3 77 79 -63 -945 -945 -945 169 3 118 -945 -945 62 18 120 -945 -96 -945 152 37 -945 150 -945 -63 -96 -945 120 96 -945 199 -945 -945 -945 -945 -945 218 -945 -945 -945 -945 184 -945 120 96 -945 118 -945 96 -945 -945 -80 195 -945 -82 20 96 -96 -82 79 -945 62 18 152 -945 -945 -945 152 37 -945 -82 -945 195 -945 -945 -945 -945 184 -945 201 -945 -945 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 7 E= 3.0e-001 0.000000 0.714286 0.000000 0.285714 0.428571 0.428571 0.142857 0.000000 0.000000 0.000000 0.714286 0.285714 0.571429 0.000000 0.000000 0.428571 0.285714 0.571429 0.000000 0.142857 0.000000 0.714286 0.285714 0.000000 0.714286 0.000000 0.142857 0.142857 0.000000 0.571429 0.428571 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.571429 0.428571 0.000000 0.571429 0.000000 0.428571 0.000000 0.000000 0.142857 0.857143 0.000000 0.142857 0.285714 0.428571 0.142857 0.142857 0.428571 0.000000 0.428571 0.285714 0.714286 0.000000 0.000000 0.000000 0.714286 0.285714 0.000000 0.142857 0.000000 0.857143 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CT][AC][GT][AT][CA][CG]A[CG]AGT[CG][AG]G[GC][CT][CA][CG]GTC -------------------------------------------------------------------------------- Time 3.93 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 20 sites = 6 llr = 108 E-value = 4.3e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :2283a:::::23:::::5a pos.-specific C ::5:3:2523a3::::8::: probability G :83:3:2:85:23::::a5: matrix T a::2::75:2:33aaa2::: bits 2.2 * 2.0 * * * * 1.7 * * * *** * * 1.5 ** * * * *** * * Relative 1.3 ** * * * * ***** * Entropy 1.1 ** * * * * ******* (26.0 bits) 0.9 ** * * ** * ******* 0.7 **** ****** ******* 0.4 *********** ******** 0.2 *********** ******** 0.0 -------------------- Multilevel TGCAAATCGGCCATTTCGAA consensus G C T C TG G sequence G T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- -------------------- 49812 354 6.53e-13 CGGATGTTTG TGCAGATCGGCCGTTTCGGA TTTCTACACC 48042 237 6.53e-13 CGGATGTTTG TGCAGATCGGCCGTTTCGGA TTTCTACACC 50065 228 7.52e-09 TCTTCCCAGT TGGAAATTCCCGATTTCGAA GGGGTATCGA 37858 159 7.52e-09 AGCGTGTCTA TACACATTGTCTATTTCGAA TTTCGAACGG 33631 405 1.72e-08 CTGTCTTGCG TGAAAAGTGGCTTTTTTGAA CGGACCGTGT 48755 243 1.72e-08 ATCCTCACCA TGGTCACCGCCATTTTCGGA CACAGGTAAC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 49812 6.5e-13 353_[+3]_127 48042 6.5e-13 236_[+3]_244 50065 7.5e-09 227_[+3]_253 37858 7.5e-09 158_[+3]_322 33631 1.7e-08 404_[+3]_76 48755 1.7e-08 242_[+3]_238 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=20 seqs=6 49812 ( 354) TGCAGATCGGCCGTTTCGGA 1 48042 ( 237) TGCAGATCGGCCGTTTCGGA 1 50065 ( 228) TGGAAATTCCCGATTTCGAA 1 37858 ( 159) TACACATTGTCTATTTCGAA 1 33631 ( 405) TGAAAAGTGGCTTTTTTGAA 1 48755 ( 243) TGGTCACCGCCATTTTCGGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 20 n= 7696 bayes= 9.98247 E= 4.3e+000 -923 -923 -923 184 -60 -923 191 -923 -60 101 59 -923 172 -923 -923 -74 40 42 59 -923 199 -923 -923 -923 -923 -57 -41 126 -923 101 -923 84 -923 -57 191 -923 -923 42 118 -74 -923 201 -923 -923 -60 42 -41 26 40 -923 59 26 -923 -923 -923 184 -923 -923 -923 184 -923 -923 -923 184 -923 175 -923 -74 -923 -923 218 -923 99 -923 118 -923 199 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 20 nsites= 6 E= 4.3e+000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.833333 0.000000 0.166667 0.500000 0.333333 0.000000 0.833333 0.000000 0.000000 0.166667 0.333333 0.333333 0.333333 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.166667 0.166667 0.666667 0.000000 0.500000 0.000000 0.500000 0.000000 0.166667 0.833333 0.000000 0.000000 0.333333 0.500000 0.166667 0.000000 1.000000 0.000000 0.000000 0.166667 0.333333 0.166667 0.333333 0.333333 0.000000 0.333333 0.333333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.833333 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TG[CG]A[ACG]AT[CT]G[GC]C[CT][AGT]TTTCG[AG]A -------------------------------------------------------------------------------- Time 5.85 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 37858 1.40e-07 158_[+3(7.52e-09)]_15_\ [+1(3.57e-07)]_295 48173 1.25e-02 275_[+1(1.24e-06)]_213 15063 1.10e-02 202_[+1(5.32e-06)]_286 15214 3.69e-03 286_[+1(3.57e-07)]_202 48755 4.57e-10 166_[+2(3.92e-10)]_55_\ [+3(1.72e-08)]_238 55069 3.89e-03 294_[+1(3.87e-06)]_194 23811 6.44e-05 2_[+2(2.10e-08)]_477 16698 9.87e-03 91_[+1(1.01e-06)]_397 54169 1.05e-07 186_[+1(3.57e-07)]_130_\ [+2(7.52e-09)]_151 18808 7.34e-01 500 33631 4.08e-06 323_[+1(6.20e-06)]_69_\ [+3(1.72e-08)]_76 39325 4.28e-05 127_[+2(4.62e-09)]_352 32160 1.02e-06 120_[+2(3.74e-08)]_210_\ [+1(6.14e-07)]_137 50065 6.32e-05 227_[+3(7.52e-09)]_253 48042 1.34e-14 236_[+3(6.53e-13)]_53_\ [+2(1.20e-10)]_170 49812 1.23e-14 353_[+3(6.53e-13)]_53_\ [+2(1.20e-10)]_53 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************