******************************************************************************** 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/44/44.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 10082 1.0000 500 11283 1.0000 500 1131 1.0000 500 13887 1.0000 500 23262 1.0000 500 23415 1.0000 500 23934 1.0000 500 2434 1.0000 500 6178 1.0000 500 6365 1.0000 500 6457 1.0000 500 bd1472 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/44/44.seqs.fa -oc motifs/44 -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= 12 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= 6000 N= 12 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.259 C 0.236 G 0.232 T 0.274 Background letter frequencies (from dataset with add-one prior applied): A 0.259 C 0.236 G 0.232 T 0.274 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 21 sites = 12 llr = 157 E-value = 2.7e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::2234182a3:84553:451 pos.-specific C 5637818:4:763445186:9 probability G 135::22:4:14::::3::3: matrix T 42:2:3:3:::::21:32:3: bits 2.1 1.9 * 1.7 * * 1.5 * * * Relative 1.3 * * * * * Entropy 1.1 * ** * ** * ** * (18.9 bits) 0.8 ** ** **** * ** * 0.6 ***** ******* ** ** * 0.4 ***** ********** **** 0.2 ********************* 0.0 --------------------- Multilevel CCGCCACACACCAAAAACCAC consensus TGC AT TG AGCCCCG AG sequence T T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 13887 165 3.83e-10 CCTCCTTCCT CCGCCACACAACAAACGCAAC GGTCATACAA 23934 248 9.41e-09 CTTGACGACA CCACCTCACACGACCAGCAGC CACCCACCTT 6457 420 1.45e-08 TCACAGTCTC CGCCCACACACCCACCACCTC TCCACTCTCA 23262 330 1.66e-08 CTCGTCTCCC CCCCCGCAGACGACACCCAAC CACGAAACTG bd1472 198 1.75e-07 CAACTCGTCA CGCACACAAAACAACAACCAC AACGACCACC 1131 430 5.32e-07 AGTTTATGCA GTGACTCAGAACACACACCAC TCACTCTCGG 11283 103 6.82e-07 TTCTCATTTG TCGTATCTCACGAACATCCTC TGCAGTAACA 2434 423 8.66e-07 CATTTCAGTC TCCCCTCTAACCCCAATTCAC TTGCCAGTGC 6178 311 1.46e-06 ACGGACGGGG CGGCAAGAGAGGAAAAACAGC TTCTTTCTTT 23415 287 2.48e-06 TGTGCAGCAG TTGCAGCAGACGATCCGTCTC TTGATGTTTT 10082 459 4.70e-06 GACCCTTCAT TCACCAGTGACCCTTCGCCGC CTTCTCTTAG 6365 382 5.50e-06 CTCACTTGCA TCGTCCAACACCACAATCAAA TTCCGATCAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13887 3.8e-10 164_[+1]_315 23934 9.4e-09 247_[+1]_232 6457 1.4e-08 419_[+1]_60 23262 1.7e-08 329_[+1]_150 bd1472 1.8e-07 197_[+1]_282 1131 5.3e-07 429_[+1]_50 11283 6.8e-07 102_[+1]_377 2434 8.7e-07 422_[+1]_57 6178 1.5e-06 310_[+1]_169 23415 2.5e-06 286_[+1]_193 10082 4.7e-06 458_[+1]_21 6365 5.5e-06 381_[+1]_98 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=21 seqs=12 13887 ( 165) CCGCCACACAACAAACGCAAC 1 23934 ( 248) CCACCTCACACGACCAGCAGC 1 6457 ( 420) CGCCCACACACCCACCACCTC 1 23262 ( 330) CCCCCGCAGACGACACCCAAC 1 bd1472 ( 198) CGCACACAAAACAACAACCAC 1 1131 ( 430) GTGACTCAGAACACACACCAC 1 11283 ( 103) TCGTATCTCACGAACATCCTC 1 2434 ( 423) TCCCCTCTAACCCCAATTCAC 1 6178 ( 311) CGGCAAGAGAGGAAAAACAGC 1 23415 ( 287) TTGCAGCAGACGATCCGTCTC 1 10082 ( 459) TCACCAGTGACCCTTCGCCGC 1 6365 ( 382) TCGTCCAACACCACAATCAAA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 5760 bayes= 9.35214 E= 2.7e-001 -1023 108 -147 60 -1023 131 11 -72 -63 50 111 -1023 -63 150 -1023 -72 -5 167 -1023 -1023 69 -150 -47 28 -163 167 -47 -1023 154 -1023 -1023 -13 -63 82 85 -1023 195 -1023 -1023 -1023 -5 150 -147 -1023 -1023 131 85 -1023 154 9 -1023 -1023 69 82 -1023 -72 95 82 -1023 -172 95 108 -1023 -1023 37 -150 53 -13 -1023 182 -1023 -72 69 131 -1023 -1023 95 -1023 11 -13 -163 196 -1023 -1023 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 12 E= 2.7e-001 0.000000 0.500000 0.083333 0.416667 0.000000 0.583333 0.250000 0.166667 0.166667 0.333333 0.500000 0.000000 0.166667 0.666667 0.000000 0.166667 0.250000 0.750000 0.000000 0.000000 0.416667 0.083333 0.166667 0.333333 0.083333 0.750000 0.166667 0.000000 0.750000 0.000000 0.000000 0.250000 0.166667 0.416667 0.416667 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.666667 0.083333 0.000000 0.000000 0.583333 0.416667 0.000000 0.750000 0.250000 0.000000 0.000000 0.416667 0.416667 0.000000 0.166667 0.500000 0.416667 0.000000 0.083333 0.500000 0.500000 0.000000 0.000000 0.333333 0.083333 0.333333 0.250000 0.000000 0.833333 0.000000 0.166667 0.416667 0.583333 0.000000 0.000000 0.500000 0.000000 0.250000 0.250000 0.083333 0.916667 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [CT][CG][GC]C[CA][AT]C[AT][CG]A[CA][CG][AC][AC][AC][AC][AGT]C[CA][AGT]C -------------------------------------------------------------------------------- Time 1.34 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 17 sites = 6 llr = 96 E-value = 2.6e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 822:52:5:7a7:57:a pos.-specific C :2::::::23:3::2:: probability G :77a28a38:::a5:a: matrix T 2:2:3::2::::::2:: bits 2.1 * * * * 1.9 * * * * ** 1.7 * * * * ** 1.5 * ** * * * ** Relative 1.3 * * ** * * * ** Entropy 1.1 * * ** ****** ** (23.1 bits) 0.8 **** ** ****** ** 0.6 **** ************ 0.4 ***************** 0.2 ***************** 0.0 ----------------- Multilevel AGGGAGGAGAAAGAAGA consensus T G C C G sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ----------------- 13887 272 9.08e-09 TGACGTAGAC AAGGTGGAGAACGGAGA GGCGGCTGCT 6365 246 1.10e-08 GTTAGTATGC ACGGAGGTGAAAGAAGA CCGTCGATTA 6178 198 1.74e-08 GAAGAGGTGT AGGGAGGACAAAGGTGA TGGTATGTGT 23415 392 2.54e-08 ATCGTTGAAG AGAGGGGGGAACGGAGA GAGGCAACAA bd1472 336 4.61e-08 ACATGGCCAG AGGGAAGGGCAAGACGA TCCCCATCAA 2434 282 6.59e-08 CGCAGTTACT TGTGTGGAGCAAGAAGA AGTCTACAAT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 13887 9.1e-09 271_[+2]_212 6365 1.1e-08 245_[+2]_238 6178 1.7e-08 197_[+2]_286 23415 2.5e-08 391_[+2]_92 bd1472 4.6e-08 335_[+2]_148 2434 6.6e-08 281_[+2]_202 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=17 seqs=6 13887 ( 272) AAGGTGGAGAACGGAGA 1 6365 ( 246) ACGGAGGTGAAAGAAGA 1 6178 ( 198) AGGGAGGACAAAGGTGA 1 23415 ( 392) AGAGGGGGGAACGGAGA 1 bd1472 ( 336) AGGGAAGGGCAAGACGA 1 2434 ( 282) TGTGTGGAGCAAGAAGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 17 n= 5808 bayes= 10.3652 E= 2.6e+000 169 -923 -923 -72 -63 -50 152 -923 -63 -923 152 -72 -923 -923 211 -923 95 -923 -47 28 -63 -923 185 -923 -923 -923 211 -923 95 -923 53 -72 -923 -50 185 -923 136 50 -923 -923 195 -923 -923 -923 136 50 -923 -923 -923 -923 211 -923 95 -923 111 -923 136 -50 -923 -72 -923 -923 211 -923 195 -923 -923 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 17 nsites= 6 E= 2.6e+000 0.833333 0.000000 0.000000 0.166667 0.166667 0.166667 0.666667 0.000000 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.166667 0.333333 0.166667 0.000000 0.833333 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.333333 0.166667 0.000000 0.166667 0.833333 0.000000 0.666667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.500000 0.000000 0.500000 0.000000 0.666667 0.166667 0.000000 0.166667 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- AGGG[AT]GG[AG]G[AC]A[AC]G[AG]AGA -------------------------------------------------------------------------------- Time 2.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 12 sites = 12 llr = 117 E-value = 4.2e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::9:::1:3::: pos.-specific C :1:::32:2::: probability G 19::8134248: matrix T 9:1a3746362a bits 2.1 1.9 * * 1.7 * * * 1.5 **** ** Relative 1.3 ***** ** Entropy 1.1 ***** * *** (14.1 bits) 0.8 ****** * *** 0.6 ****** * *** 0.4 ****** * *** 0.2 ******** *** 0.0 ------------ Multilevel TGATGTTTATGT consensus TCGGTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 23415 309 2.82e-07 ATCCGTCTCT TGATGTTTTTGT AGCCCGAGAA 6457 92 1.06e-06 GTTTGCCTCT TGATGTGTTGGT GATTTGCATC 1131 239 3.03e-06 ACGTGATGGT TGATGTCGATGT TGTTTGTTCC 23934 7 6.05e-06 CTGCTG TGATTTGGATGT AGTCTAGCAA bd1472 72 6.69e-06 GGGGATGAAA TGATTTGTTGGT CTGGGGGGGT 23262 51 7.28e-06 GCATCCGTCA TGATGCCGATGT TCGTTGTATG 6365 14 1.18e-05 GCCTTTCTGA TGATTCTTTTGT ACATTGATAT 6178 226 1.80e-05 GGTATGTGTG TGATGTTTGGTT GATTGATGGT 11283 43 2.68e-05 AAGTGCCACA TGATGCATCTGT TGGTTGTGAT 2434 233 3.80e-05 TGATGCATCG TCATGTTGGGGT GCACGCTGTG 13887 362 8.64e-05 ACGGTGCAAT GGATGTGTCTTT TGCAAATCGT 10082 86 8.64e-05 GAAAGTTCTT TGTTGGTGAGGT ATGTCAGATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 23415 2.8e-07 308_[+3]_180 6457 1.1e-06 91_[+3]_397 1131 3e-06 238_[+3]_250 23934 6e-06 6_[+3]_482 bd1472 6.7e-06 71_[+3]_417 23262 7.3e-06 50_[+3]_438 6365 1.2e-05 13_[+3]_475 6178 1.8e-05 225_[+3]_263 11283 2.7e-05 42_[+3]_446 2434 3.8e-05 232_[+3]_256 13887 8.6e-05 361_[+3]_127 10082 8.6e-05 85_[+3]_403 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=12 seqs=12 23415 ( 309) TGATGTTTTTGT 1 6457 ( 92) TGATGTGTTGGT 1 1131 ( 239) TGATGTCGATGT 1 23934 ( 7) TGATTTGGATGT 1 bd1472 ( 72) TGATTTGTTGGT 1 23262 ( 51) TGATGCCGATGT 1 6365 ( 14) TGATTCTTTTGT 1 6178 ( 226) TGATGTTTGGTT 1 11283 ( 43) TGATGCATCTGT 1 2434 ( 233) TCATGTTGGGGT 1 13887 ( 362) GGATGTGTCTTT 1 10082 ( 86) TGTTGGTGAGGT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 5868 bayes= 8.93074 E= 4.2e+000 -1023 -1023 -147 174 -1023 -150 198 -1023 182 -1023 -1023 -172 -1023 -1023 -1023 187 -1023 -1023 169 -13 -1023 9 -147 128 -163 -50 53 60 -1023 -1023 85 109 37 -50 -47 28 -1023 -1023 85 109 -1023 -1023 185 -72 -1023 -1023 -1023 187 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 4.2e+000 0.000000 0.000000 0.083333 0.916667 0.000000 0.083333 0.916667 0.000000 0.916667 0.000000 0.000000 0.083333 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.250000 0.083333 0.666667 0.083333 0.166667 0.333333 0.416667 0.000000 0.000000 0.416667 0.583333 0.333333 0.166667 0.166667 0.333333 0.000000 0.000000 0.416667 0.583333 0.000000 0.000000 0.833333 0.166667 0.000000 0.000000 0.000000 1.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- TGAT[GT][TC][TG][TG][AT][TG]GT -------------------------------------------------------------------------------- Time 3.78 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 10082 1.89e-03 85_[+3(8.64e-05)]_361_\ [+1(4.70e-06)]_21 11283 4.83e-05 42_[+3(2.68e-05)]_48_[+1(6.82e-07)]_\ 377 1131 2.85e-05 238_[+3(3.03e-06)]_179_\ [+1(5.32e-07)]_50 13887 1.72e-11 164_[+1(3.83e-10)]_19_\ [+1(8.32e-05)]_46_[+2(9.08e-09)]_73_[+3(8.64e-05)]_89_[+1(2.00e-05)]_17 23262 3.34e-06 50_[+3(7.28e-06)]_267_\ [+1(1.66e-08)]_27_[+1(3.82e-05)]_102 23415 7.89e-10 286_[+1(2.48e-06)]_1_[+3(2.82e-07)]_\ 71_[+2(2.54e-08)]_92 23934 6.71e-07 6_[+3(6.05e-06)]_229_[+1(9.41e-09)]_\ 2_[+1(5.29e-05)]_209 2434 6.54e-08 232_[+3(3.80e-05)]_37_\ [+2(6.59e-08)]_124_[+1(8.66e-07)]_57 6178 1.57e-08 197_[+2(1.74e-08)]_11_\ [+3(1.80e-05)]_73_[+1(1.46e-06)]_169 6365 2.37e-08 13_[+3(1.18e-05)]_220_\ [+2(1.10e-08)]_119_[+1(5.50e-06)]_98 6457 7.43e-07 91_[+3(1.06e-06)]_316_\ [+1(1.45e-08)]_60 bd1472 2.21e-09 71_[+3(6.69e-06)]_82_[+1(6.60e-05)]_\ 11_[+1(1.75e-07)]_117_[+2(4.61e-08)]_148 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************