******************************************************************************** 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/365/365.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 47597 1.0000 500 7337 1.0000 500 49559 1.0000 500 40753 1.0000 500 44256 1.0000 500 44835 1.0000 500 44838 1.0000 500 12416 1.0000 500 46243 1.0000 500 48210 1.0000 500 47400 1.0000 500 49880 1.0000 500 49164 1.0000 500 44285 1.0000 500 33916 1.0000 500 43879 1.0000 500 43687 1.0000 500 49834 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/365/365.seqs.fa -oc motifs/365 -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= 18 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= 9000 N= 18 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.282 C 0.237 G 0.212 T 0.269 Background letter frequencies (from dataset with add-one prior applied): A 0.282 C 0.237 G 0.212 T 0.269 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 16 llr = 156 E-value = 1.9e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A 9383::9a84:1 pos.-specific C 16::a11::154 probability G :1:::9::231: matrix T ::37:::::345 bits 2.2 2.0 * 1.8 * * 1.6 * **** Relative 1.3 * **** Entropy 1.1 * * ***** (14.1 bits) 0.9 ********* 0.7 ********* * 0.4 ********* ** 0.2 ************ 0.0 ------------ Multilevel ACATCGAAAACT consensus ATA GTC sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 44838 233 5.58e-07 CTGGCGAGAG ACATCGAAAATC AACACGAACC 44835 236 5.58e-07 CTGGCGAGAG ACATCGAAAATC AACACGAACC 44256 392 2.08e-06 ATCGGAAAAC AAATCGAAAGCT GTCGACTTTG 12416 226 2.42e-06 GCTTTCACTA ACAACGAAAATC GTTTGAAGAG 44285 383 5.45e-06 ACCAGTGCAA ACATCGAAACCT GAGAAGCAAC 48210 387 7.17e-06 CGAAAACCGG ACTACGAAAACC AGATTTTGAA 49834 43 7.97e-06 TGGCGACAAT AAATCGAAGACT CTAAAGGAGT 40753 18 1.30e-05 AACGCAGCAA ACTACGAAATCC CACAAATTAT 7337 355 1.30e-05 TCGGTTGACG ACAACGAAGTCT GTTTCGGGTT 47400 299 1.88e-05 ATTAATGAAT AAATCGAAAGTA GCTCACTTCA 49164 79 2.05e-05 CAGACAAACT ACATCGCAATCT TTGATTTCCG 49880 201 2.68e-05 TGAAACCCTC AAATCGAAATGT CCGACCACGA 49559 29 2.94e-05 ACATGGCATC AAATCCAAAATC CTGAGCTCTT 46243 363 4.77e-05 TGAAACCTTA CCTTCGAAAGTT CGGTTTCTCG 43687 145 5.95e-05 TGTAAGACAG ACAACCAAGGCT AGGGACAAGG 33916 270 8.73e-05 TAGTTTAAAT AGTTCGAAAATA TAACAATATA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44838 5.6e-07 232_[+1]_256 44835 5.6e-07 235_[+1]_253 44256 2.1e-06 391_[+1]_97 12416 2.4e-06 225_[+1]_263 44285 5.4e-06 382_[+1]_106 48210 7.2e-06 386_[+1]_102 49834 8e-06 42_[+1]_446 40753 1.3e-05 17_[+1]_471 7337 1.3e-05 354_[+1]_134 47400 1.9e-05 298_[+1]_190 49164 2e-05 78_[+1]_410 49880 2.7e-05 200_[+1]_288 49559 2.9e-05 28_[+1]_460 46243 4.8e-05 362_[+1]_126 43687 5.9e-05 144_[+1]_344 33916 8.7e-05 269_[+1]_219 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=16 44838 ( 233) ACATCGAAAATC 1 44835 ( 236) ACATCGAAAATC 1 44256 ( 392) AAATCGAAAGCT 1 12416 ( 226) ACAACGAAAATC 1 44285 ( 383) ACATCGAAACCT 1 48210 ( 387) ACTACGAAAACC 1 49834 ( 43) AAATCGAAGACT 1 40753 ( 18) ACTACGAAATCC 1 7337 ( 355) ACAACGAAGTCT 1 47400 ( 299) AAATCGAAAGTA 1 49164 ( 79) ACATCGCAATCT 1 49880 ( 201) AAATCGAAATGT 1 49559 ( 29) AAATCCAAAATC 1 46243 ( 363) CCTTCGAAAGTT 1 43687 ( 145) ACAACCAAGGCT 1 33916 ( 270) AGTTCGAAAATA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 8802 bayes= 9.10099 E= 1.9e-001 173 -192 -1064 -1064 15 140 -176 -1064 141 -1064 -1064 -11 15 -1064 -1064 135 -1064 208 -1064 -1064 -1064 -92 205 -1064 173 -192 -1064 -1064 183 -1064 -1064 -1064 153 -1064 -18 -1064 63 -192 24 -11 -1064 108 -176 70 -117 66 -1064 89 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 1.9e-001 0.937500 0.062500 0.000000 0.000000 0.312500 0.625000 0.062500 0.000000 0.750000 0.000000 0.000000 0.250000 0.312500 0.000000 0.000000 0.687500 0.000000 1.000000 0.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.937500 0.062500 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.812500 0.000000 0.187500 0.000000 0.437500 0.062500 0.250000 0.250000 0.000000 0.500000 0.062500 0.437500 0.125000 0.375000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- A[CA][AT][TA]CGAAA[AGT][CT][TC] -------------------------------------------------------------------------------- Time 2.89 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 4 llr = 94 E-value = 8.1e-001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A ::::::::5:5::a::3:::a pos.-specific C 5::::a3:58::8:a3::a:: probability G 5:::a::a:3:a3::3:5:a: matrix T :aaa::8:::5::::585::: bits 2.2 * * * * 2.0 ** * * * ** 1.8 ***** * * ** *** 1.6 ***** * * ** *** Relative 1.3 ***** * * **** *** Entropy 1.1 ******** * **** ***** (33.9 bits) 0.9 *************** ***** 0.7 *************** ***** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel CTTTGCTGACAGCACTTGCGA consensus G C CGT G CAT sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44838 295 1.30e-13 TTTCGATTGG GTTTGCTGCCTGCACTTGCGA TCGGTGACAC 44835 298 1.30e-13 TTTCGATTGG GTTTGCTGCCTGCACTTGCGA TCGGTGACAC 7337 248 3.82e-11 GCGCGTCCAG CTTTGCCGACAGCACCTTCGA CTACCGTAGT 44256 409 9.74e-11 AAGCTGTCGA CTTTGCTGAGAGGACGATCGA ACATCAAAGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44838 1.3e-13 294_[+2]_185 44835 1.3e-13 297_[+2]_182 7337 3.8e-11 247_[+2]_232 44256 9.7e-11 408_[+2]_71 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=4 44838 ( 295) GTTTGCTGCCTGCACTTGCGA 1 44835 ( 298) GTTTGCTGCCTGCACTTGCGA 1 7337 ( 248) CTTTGCCGACAGCACCTTCGA 1 44256 ( 409) CTTTGCTGAGAGGACGATCGA 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8640 bayes= 11.0761 E= 8.1e-001 -865 107 124 -865 -865 -865 -865 189 -865 -865 -865 189 -865 -865 -865 189 -865 -865 224 -865 -865 207 -865 -865 -865 8 -865 148 -865 -865 224 -865 82 107 -865 -865 -865 166 24 -865 82 -865 -865 89 -865 -865 224 -865 -865 166 24 -865 182 -865 -865 -865 -865 207 -865 -865 -865 8 24 89 -17 -865 -865 148 -865 -865 124 89 -865 207 -865 -865 -865 -865 224 -865 182 -865 -865 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 8.1e-001 0.000000 0.500000 0.500000 0.000000 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 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.500000 0.000000 0.000000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 0.750000 0.250000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.250000 0.500000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 0.500000 0.500000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [CG]TTTGC[TC]G[AC][CG][AT]G[CG]AC[TCG][TA][GT]CGA -------------------------------------------------------------------------------- Time 5.71 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 4 llr = 92 E-value = 1.5e+000 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :5:::::::::a33:a::::: pos.-specific C 35::8:5::5a:::::a:3:8 probability G 8::5:a5:a5::::a:::883 matrix T ::a53::a::::88:::a:3: bits 2.2 * * * 2.0 * * * * * 1.8 * * ** ** **** 1.6 * * ** ** **** Relative 1.3 * * * ** ** ******* Entropy 1.1 * ******************* (33.3 bits) 0.9 ********************* 0.7 ********************* 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel GATGCGCTGCCATTGACTGGC consensus CC TT G G AA CTG sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44838 207 1.01e-12 GTTGCATGAA GATTCGGTGGCATTGACTGGC GAGAGACATC 44835 210 1.01e-12 GTTGCATGAA GATTCGGTGGCATTGACTGGC GAGAGACATC 12416 139 2.86e-11 TCGTACTAAT GCTGCGCTGCCATTGACTGTG AGTTGAACAA 7337 132 2.30e-10 GCCTCTCAAT CCTGTGCTGCCAAAGACTCGC GCGGAGAGTG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44838 1e-12 206_[+3]_273 44835 1e-12 209_[+3]_270 12416 2.9e-11 138_[+3]_341 7337 2.3e-10 131_[+3]_348 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=4 44838 ( 207) GATTCGGTGGCATTGACTGGC 1 44835 ( 210) GATTCGGTGGCATTGACTGGC 1 12416 ( 139) GCTGCGCTGCCATTGACTGTG 1 7337 ( 132) CCTGTGCTGCCAAAGACTCGC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 8640 bayes= 11.0761 E= 1.5e+000 -865 8 182 -865 82 107 -865 -865 -865 -865 -865 189 -865 -865 124 89 -865 166 -865 -11 -865 -865 224 -865 -865 107 124 -865 -865 -865 -865 189 -865 -865 224 -865 -865 107 124 -865 -865 207 -865 -865 182 -865 -865 -865 -17 -865 -865 148 -17 -865 -865 148 -865 -865 224 -865 182 -865 -865 -865 -865 207 -865 -865 -865 -865 -865 189 -865 8 182 -865 -865 -865 182 -11 -865 166 24 -865 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 4 E= 1.5e+000 0.000000 0.250000 0.750000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.750000 0.000000 0.250000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.250000 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.750000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.250000 0.750000 0.000000 0.000000 0.000000 0.750000 0.250000 0.000000 0.750000 0.250000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GC][AC]T[GT][CT]G[CG]TG[CG]CA[TA][TA]GACT[GC][GT][CG] -------------------------------------------------------------------------------- Time 8.53 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 47597 7.75e-01 500 7337 1.03e-14 131_[+3(2.30e-10)]_95_\ [+2(3.82e-11)]_86_[+1(1.30e-05)]_134 49559 8.14e-02 28_[+1(2.94e-05)]_460 40753 3.64e-02 17_[+1(1.30e-05)]_471 44256 1.17e-08 391_[+1(2.08e-06)]_5_[+2(9.74e-11)]_\ 71 44835 1.21e-20 209_[+3(1.01e-12)]_5_[+1(5.58e-07)]_\ 50_[+2(1.30e-13)]_182 44838 1.21e-20 206_[+3(1.01e-12)]_5_[+1(5.58e-07)]_\ 50_[+2(1.30e-13)]_185 12416 2.50e-09 138_[+3(2.86e-11)]_66_\ [+1(2.42e-06)]_110_[+3(8.45e-05)]_132 46243 3.44e-02 362_[+1(4.77e-05)]_126 48210 2.94e-02 386_[+1(7.17e-06)]_102 47400 1.20e-01 298_[+1(1.88e-05)]_190 49880 1.54e-01 200_[+1(2.68e-05)]_288 49164 1.43e-02 78_[+1(2.05e-05)]_410 44285 2.49e-02 382_[+1(5.45e-06)]_106 33916 1.65e-01 269_[+1(8.73e-05)]_219 43879 9.38e-01 500 43687 1.86e-01 144_[+1(5.95e-05)]_344 49834 4.33e-02 42_[+1(7.97e-06)]_55_[+1(9.19e-05)]_\ 379 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************