******************************************************************************** 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/206/206.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 31942 1.0000 500 43160 1.0000 500 48999 1.0000 500 55162 1.0000 500 44700 1.0000 500 45293 1.0000 500 20716 1.0000 500 42949 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/206/206.seqs.fa -oc motifs/206 -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= 8 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= 4000 N= 8 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.273 C 0.238 G 0.225 T 0.264 Background letter frequencies (from dataset with add-one prior applied): A 0.273 C 0.238 G 0.225 T 0.264 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 8 llr = 86 E-value = 1.5e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A ::1a:1:8:51: pos.-specific C ::1:a9::::44 probability G 8:8:::a:5445 matrix T 3a:::::35111 bits 2.2 * * 1.9 * ** * 1.7 * ** * 1.5 * **** Relative 1.3 ** **** Entropy 1.1 ********* (15.5 bits) 0.9 ********* 0.6 ********** * 0.4 ********** * 0.2 ************ 0.0 ------------ Multilevel GTGACCGAGACG consensus T TTGGC sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 20716 426 4.42e-07 CGAATACGTG GTGACCGAGGGC TAGCGGGATG 45293 438 5.28e-07 CCCATTAGAC GTGACCGATAGC AGCCTGCATT 43160 318 2.33e-06 ATGCGAACTC TTGACCGAGAGC GTCTCGAACA 48999 237 4.75e-06 CGTGTGAAAT GTAACCGATGCG AAGCCGATTG 55162 473 6.34e-06 AGTAAGCTCT TTGACCGAGAAG ACAGGAACGT 44700 388 1.14e-05 GCCCAAATTT GTCACCGTTACG GAGTCAATCG 42949 70 1.95e-05 ATAATCGGAA GTGACCGTTTTG CCACGACTTA 31942 263 2.07e-05 GTAACCAAGC GTGACAGAGGCT TATTCAGTGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 20716 4.4e-07 425_[+1]_63 45293 5.3e-07 437_[+1]_51 43160 2.3e-06 317_[+1]_171 48999 4.8e-06 236_[+1]_252 55162 6.3e-06 472_[+1]_16 44700 1.1e-05 387_[+1]_101 42949 2e-05 69_[+1]_419 31942 2.1e-05 262_[+1]_226 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=8 20716 ( 426) GTGACCGAGGGC 1 45293 ( 438) GTGACCGATAGC 1 43160 ( 318) TTGACCGAGAGC 1 48999 ( 237) GTAACCGATGCG 1 55162 ( 473) TTGACCGAGAAG 1 44700 ( 388) GTCACCGTTACG 1 42949 ( 70) GTGACCGTTTTG 1 31942 ( 263) GTGACAGAGGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 3912 bayes= 9.66888 E= 1.5e+002 -965 -965 173 -8 -965 -965 -965 192 -112 -93 173 -965 187 -965 -965 -965 -965 207 -965 -965 -112 188 -965 -965 -965 -965 215 -965 146 -965 -965 -8 -965 -965 115 92 87 -965 73 -108 -112 65 73 -108 -965 65 115 -108 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 8 E= 1.5e+002 0.000000 0.000000 0.750000 0.250000 0.000000 0.000000 0.000000 1.000000 0.125000 0.125000 0.750000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.125000 0.875000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.750000 0.000000 0.000000 0.250000 0.000000 0.000000 0.500000 0.500000 0.500000 0.000000 0.375000 0.125000 0.125000 0.375000 0.375000 0.125000 0.000000 0.375000 0.500000 0.125000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [GT]TGACCG[AT][GT][AG][CG][GC] -------------------------------------------------------------------------------- Time 0.53 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 21 sites = 8 llr = 116 E-value = 5.2e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 593:418454:915191:::: pos.-specific C 5::64::546a1656:44691 probability G :11:39111:::::3:::1:3 matrix T ::64::1:::::3::156316 bits 2.2 * 1.9 * 1.7 * 1.5 * * * Relative 1.3 * * ** * * Entropy 1.1 ** * * *** * * * * (20.9 bits) 0.9 ** * ** *** *** * * 0.6 **** **************** 0.4 ********************* 0.2 ********************* 0.0 --------------------- Multilevel AATCAGACACCACACATTCCT consensus C ATC ACA TCG CCT G sequence G -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 44700 188 2.47e-11 CTTTGTCCCG CATCAGACACCACCCACCCCT TTCACTCTAG 48999 292 3.00e-09 ATTTTGGAAG AATCCGAACCCACACAATCCG AGTATTGGGA 42949 428 6.71e-08 ACCCAGTCTC CGTCCGTGCCCACACATTCCT CACGAGAAAA 31942 442 2.29e-07 AATCCGCCAA AAACAGGCCCCATCGACCTCT TTGCTTATCG 20716 381 2.65e-07 GCCAAAAAAG CATTCGAAAACATCAACTCTT CTCATTTTCT 43160 479 2.84e-07 ACTAGCTAAC AAACAAACAACACACATTTCC A 55162 387 3.75e-07 CTCGTTACTA CAGTGGACGACCCACATTCCG CACGGAAAGA 45293 363 7.47e-07 AAAACGGAAA AATTGGAAACCAACGTTCGCT TGTCCTCTTT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 44700 2.5e-11 187_[+2]_292 48999 3e-09 291_[+2]_188 42949 6.7e-08 427_[+2]_52 31942 2.3e-07 441_[+2]_38 20716 2.6e-07 380_[+2]_99 43160 2.8e-07 478_[+2]_1 55162 3.7e-07 386_[+2]_93 45293 7.5e-07 362_[+2]_117 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=21 seqs=8 44700 ( 188) CATCAGACACCACCCACCCCT 1 48999 ( 292) AATCCGAACCCACACAATCCG 1 42949 ( 428) CGTCCGTGCCCACACATTCCT 1 31942 ( 442) AAACAGGCCCCATCGACCTCT 1 20716 ( 381) CATTCGAAAACATCAACTCTT 1 43160 ( 479) AAACAAACAACACACATTTCC 1 55162 ( 387) CAGTGGACGACCCACATTCCG 1 45293 ( 363) AATTGGAAACCAACGTTCGCT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 3840 bayes= 8.90388 E= 5.2e+002 87 107 -965 -965 168 -965 -85 -965 -13 -965 -85 124 -965 139 -965 51 46 65 15 -965 -112 -965 196 -965 146 -965 -85 -108 46 107 -85 -965 87 65 -85 -965 46 139 -965 -965 -965 207 -965 -965 168 -93 -965 -965 -112 139 -965 -8 87 107 -965 -965 -112 139 15 -965 168 -965 -965 -108 -112 65 -965 92 -965 65 -965 124 -965 139 -85 -8 -965 188 -965 -108 -965 -93 15 124 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 8 E= 5.2e+002 0.500000 0.500000 0.000000 0.000000 0.875000 0.000000 0.125000 0.000000 0.250000 0.000000 0.125000 0.625000 0.000000 0.625000 0.000000 0.375000 0.375000 0.375000 0.250000 0.000000 0.125000 0.000000 0.875000 0.000000 0.750000 0.000000 0.125000 0.125000 0.375000 0.500000 0.125000 0.000000 0.500000 0.375000 0.125000 0.000000 0.375000 0.625000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.875000 0.125000 0.000000 0.000000 0.125000 0.625000 0.000000 0.250000 0.500000 0.500000 0.000000 0.000000 0.125000 0.625000 0.250000 0.000000 0.875000 0.000000 0.000000 0.125000 0.125000 0.375000 0.000000 0.500000 0.000000 0.375000 0.000000 0.625000 0.000000 0.625000 0.125000 0.250000 0.000000 0.875000 0.000000 0.125000 0.000000 0.125000 0.250000 0.625000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [AC]A[TA][CT][ACG]GA[CA][AC][CA]CA[CT][AC][CG]A[TC][TC][CT]C[TG] -------------------------------------------------------------------------------- Time 1.05 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 15 sites = 6 llr = 80 E-value = 5.4e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A ::2::22:22::2:2 pos.-specific C 822::::a:3:a::: probability G ::55::7:52a:7:8 matrix T 2825a82:33::2a: bits 2.2 * ** 1.9 * * ** * 1.7 * * ** * 1.5 * * ** ** Relative 1.3 ** ** * ** ** Entropy 1.1 ** *** * ** ** (19.1 bits) 0.9 ** ***** ***** 0.6 ** ****** ***** 0.4 ** ****** ***** 0.2 ********* ***** 0.0 --------------- Multilevel CTGGTTGCGCGCGTG consensus T TT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 42949 298 1.03e-08 GGTGAGTCAT CTCTTTGCGCGCGTG ACCGTATTCA 20716 6 8.36e-08 ACCTG CTGGTTACGAGCGTG GTATGCGAGA 31942 65 4.72e-07 AGACCAACTC TTGTTTGCAGGCGTG ATGTCATGAC 55162 46 5.06e-07 ATTGTCGTTG CTGGTAGCTTGCTTG GACTTCATAT 43160 382 1.12e-06 ATTGACCTTG CTTGTTGCGTGCATA CATCAACAAC 48999 216 1.44e-06 GCAGCTGTTT CCATTTTCTCGCGTG TGAAATGTAA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 42949 1e-08 297_[+3]_188 20716 8.4e-08 5_[+3]_480 31942 4.7e-07 64_[+3]_421 55162 5.1e-07 45_[+3]_440 43160 1.1e-06 381_[+3]_104 48999 1.4e-06 215_[+3]_270 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=15 seqs=6 42949 ( 298) CTCTTTGCGCGCGTG 1 20716 ( 6) CTGGTTACGAGCGTG 1 31942 ( 65) TTGTTTGCAGGCGTG 1 55162 ( 46) CTGGTAGCTTGCTTG 1 43160 ( 382) CTTGTTGCGTGCATA 1 48999 ( 216) CCATTTTCTCGCGTG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 3888 bayes= 9.78568 E= 5.4e+002 -923 180 -923 -66 -923 -51 -923 166 -71 -51 115 -66 -923 -923 115 92 -923 -923 -923 192 -71 -923 -923 166 -71 -923 156 -66 -923 207 -923 -923 -71 -923 115 34 -71 48 -43 34 -923 -923 215 -923 -923 207 -923 -923 -71 -923 156 -66 -923 -923 -923 192 -71 -923 189 -923 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 6 E= 5.4e+002 0.000000 0.833333 0.000000 0.166667 0.000000 0.166667 0.000000 0.833333 0.166667 0.166667 0.500000 0.166667 0.000000 0.000000 0.500000 0.500000 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.000000 0.833333 0.166667 0.000000 0.666667 0.166667 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.500000 0.333333 0.166667 0.333333 0.166667 0.333333 0.000000 0.000000 1.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.166667 0.000000 0.666667 0.166667 0.000000 0.000000 0.000000 1.000000 0.166667 0.000000 0.833333 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- CTG[GT]TTGC[GT][CT]GCGTG -------------------------------------------------------------------------------- Time 1.58 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 31942 6.78e-08 64_[+3(4.72e-07)]_183_\ [+1(2.07e-05)]_167_[+2(2.29e-07)]_38 43160 2.47e-08 317_[+1(2.33e-06)]_52_\ [+3(1.12e-06)]_82_[+2(2.84e-07)]_1 48999 9.05e-10 215_[+3(1.44e-06)]_6_[+1(4.75e-06)]_\ 43_[+2(3.00e-09)]_188 55162 3.85e-08 45_[+3(5.06e-07)]_326_\ [+2(3.75e-07)]_65_[+1(6.34e-06)]_16 44700 5.56e-09 187_[+2(2.47e-11)]_179_\ [+1(1.14e-05)]_101 45293 1.16e-05 362_[+2(7.47e-07)]_54_\ [+1(5.28e-07)]_51 20716 4.54e-10 5_[+3(8.36e-08)]_360_[+2(2.65e-07)]_\ 24_[+1(4.42e-07)]_63 42949 6.11e-10 69_[+1(1.95e-05)]_216_\ [+3(1.03e-08)]_115_[+2(6.71e-08)]_52 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************