******************************************************************************** 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/237/237.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 8694 1.0000 500 46385 1.0000 500 54681 1.0000 500 15310 1.0000 500 54973 1.0000 500 44116 1.0000 500 50825 1.0000 500 11652 1.0000 500 34741 1.0000 500 34902 1.0000 500 3052 1.0000 500 35557 1.0000 500 2097 1.0000 500 46041 1.0000 500 36993 1.0000 500 47733 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/237/237.seqs.fa -oc motifs/237 -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 0.262 C 0.263 G 0.220 T 0.255 Background letter frequencies (from dataset with add-one prior applied): A 0.262 C 0.263 G 0.220 T 0.255 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 16 llr = 148 E-value = 3.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :::6:1:1:78: pos.-specific C :11:6:1:3::5 probability G 3:8:139:723: matrix T 891446:9:1:5 bits 2.2 2.0 1.7 1.5 ** Relative 1.3 ** *** Entropy 1.1 *** *** * (13.4 bits) 0.9 **** ******* 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel TTGACTGTGAAC consensus G TTG C GT sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 46041 311 1.10e-07 ACATTCACTG TTGACTGTGAAC ACCTTACCCA 8694 310 2.38e-06 ACGGTTGGCG GTGACGGTGAAC TCTAGCAGTA 50825 244 3.59e-06 CAATGTGAGA GTGACTGTGAGT GACCTGCGTG 3052 469 7.39e-06 AATACCCACC TTGTTGGTGGAC AAACTACCGT 44116 446 7.39e-06 TTTCTTCCTC TTGACAGTGAAT TTTACAGGGA 46385 12 9.05e-06 TACGACTTAT TTGATTCTGAAC TCATCGAAGC 15310 291 1.19e-05 AGACCGACGG TTGTCGGAGAAC TCCCGCTGGC 34902 3 1.50e-05 GA TTTACTGTCAAT CAATCGTCTT 36993 151 1.79e-05 AAATATTGAC TTGACGGTGTGT GAATGTGCGG 2097 355 2.00e-05 TGGCTTGACA GTCTCTGTGAAT TCGGTCCACA 11652 455 2.00e-05 GGGGCCGATC TTTTCTGTCAAT CGGCACGACG 54681 363 2.00e-05 CAACTTTGGC TTGTGTGTGAGT ACTGGATGAC 35557 186 6.72e-05 GTGTTGACCT TCGATGGTGTAC GCGATGTCCG 34741 80 1.20e-04 GTTGCCATCA TCGATTGTCGGC TCGTTTCCGA 47733 488 1.51e-04 GTTGTTGTTT TTGTTTCACAAT C 54973 189 1.51e-04 CCCGGCTTGG GTCTTTGTCGAC AAAAATCGCA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 46041 1.1e-07 310_[+1]_178 8694 2.4e-06 309_[+1]_179 50825 3.6e-06 243_[+1]_245 3052 7.4e-06 468_[+1]_20 44116 7.4e-06 445_[+1]_43 46385 9e-06 11_[+1]_477 15310 1.2e-05 290_[+1]_198 34902 1.5e-05 2_[+1]_486 36993 1.8e-05 150_[+1]_338 2097 2e-05 354_[+1]_134 11652 2e-05 454_[+1]_34 54681 2e-05 362_[+1]_126 35557 6.7e-05 185_[+1]_303 34741 0.00012 79_[+1]_409 47733 0.00015 487_[+1]_1 54973 0.00015 188_[+1]_300 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=16 46041 ( 311) TTGACTGTGAAC 1 8694 ( 310) GTGACGGTGAAC 1 50825 ( 244) GTGACTGTGAGT 1 3052 ( 469) TTGTTGGTGGAC 1 44116 ( 446) TTGACAGTGAAT 1 46385 ( 12) TTGATTCTGAAC 1 15310 ( 291) TTGTCGGAGAAC 1 34902 ( 3) TTTACTGTCAAT 1 36993 ( 151) TTGACGGTGTGT 1 2097 ( 355) GTCTCTGTGAAT 1 11652 ( 455) TTTTCTGTCAAT 1 54681 ( 363) TTGTGTGTGAGT 1 35557 ( 186) TCGATGGTGTAC 1 34741 ( 80) TCGATTGTCGGC 1 47733 ( 488) TTGTTTCACAAT 1 54973 ( 189) GTCTTTGTCGAC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 8.93074 E= 3.5e+001 -1064 -1064 19 155 -1064 -107 -1064 178 -1064 -107 177 -103 110 -1064 -1064 78 -1064 110 -181 55 -207 -1064 51 129 -1064 -107 199 -1064 -107 -1064 -1064 178 -1064 25 165 -1064 139 -1064 -23 -103 152 -1064 19 -1064 -1064 93 -1064 97 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 16 E= 3.5e+001 0.000000 0.000000 0.250000 0.750000 0.000000 0.125000 0.000000 0.875000 0.000000 0.125000 0.750000 0.125000 0.562500 0.000000 0.000000 0.437500 0.000000 0.562500 0.062500 0.375000 0.062500 0.000000 0.312500 0.625000 0.000000 0.125000 0.875000 0.000000 0.125000 0.000000 0.000000 0.875000 0.000000 0.312500 0.687500 0.000000 0.687500 0.000000 0.187500 0.125000 0.750000 0.000000 0.250000 0.000000 0.000000 0.500000 0.000000 0.500000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- [TG]TG[AT][CT][TG]GT[GC]A[AG][CT] -------------------------------------------------------------------------------- Time 2.31 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 12 sites = 5 llr = 67 E-value = 8.1e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A 2:::a4::a2:: pos.-specific C :::::4:::::2 probability G 8:8a::aa:4:: matrix T :a2::2:::4a8 bits 2.2 * ** 2.0 * ** *** * 1.7 * ** *** * 1.5 **** *** * Relative 1.3 ***** *** ** Entropy 1.1 ***** *** ** (19.4 bits) 0.9 ***** *** ** 0.7 ***** *** ** 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GTGGAAGGAGTT consensus A T C T C sequence T A -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 2097 130 1.46e-07 TTCGTCTCGG GTGGACGGATTT CACAGGGTCT 35557 235 1.79e-07 CTGTCGATAC GTGGATGGAGTT GGCCAGTCTC 54973 226 3.68e-07 AGAAATCGGA GTGGAAGGAGTC TCGTTCGTGG 50825 61 8.32e-07 GGAGGATTCC GTTGACGGATTT CACGTCCAAA 8694 153 1.34e-06 CTCCGTCTTG ATGGAAGGAATT GGGAATGCGA -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 2097 1.5e-07 129_[+2]_359 35557 1.8e-07 234_[+2]_254 54973 3.7e-07 225_[+2]_263 50825 8.3e-07 60_[+2]_428 8694 1.3e-06 152_[+2]_336 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=12 seqs=5 2097 ( 130) GTGGACGGATTT 1 35557 ( 235) GTGGATGGAGTT 1 54973 ( 226) GTGGAAGGAGTC 1 50825 ( 61) GTTGACGGATTT 1 8694 ( 153) ATGGAAGGAATT 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 7824 bayes= 10.8625 E= 8.1e+002 -39 -897 186 -897 -897 -897 -897 197 -897 -897 186 -35 -897 -897 218 -897 193 -897 -897 -897 61 60 -897 -35 -897 -897 218 -897 -897 -897 218 -897 193 -897 -897 -897 -39 -897 86 65 -897 -897 -897 197 -897 -39 -897 165 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 5 E= 8.1e+002 0.200000 0.000000 0.800000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.400000 0.400000 0.000000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.000000 0.400000 0.400000 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- [GA]T[GT]GA[ACT]GGA[GTA]T[TC] -------------------------------------------------------------------------------- Time 4.42 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 21 sites = 5 llr = 94 E-value = 1.5e+003 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A :::::44::::::4::4:::: pos.-specific C :2:48:4a::2a:24:2a::: probability G ::44::2:6a4:a246::8aa matrix T a86226::4:4::2244:2:: bits 2.2 * * ** 2.0 * * * ** * ** 1.7 * * * ** * ** 1.5 * * * ** **** Relative 1.3 ** * * * ** **** Entropy 1.1 *** * *** ** * **** (27.2 bits) 0.9 *** ** *** ** * **** 0.7 *** ** *** ** * **** 0.4 ************* ******* 0.2 ************* ******* 0.0 --------------------- Multilevel TTTCCTACGGGCGACGACGGG consensus CGGTAC T T CGTT T sequence T G C GT C T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------------- 36993 91 1.41e-10 ACAATGTGGC TTTCCAACGGTCGACTACGGG GAATTGCCGG 54681 147 3.27e-10 GCATTTTTTG TTTGCTGCTGGCGCGGTCGGG GAAGTATCCT 47733 297 1.46e-09 TACCGTACCC TCTCCTACTGTCGGGGACGGG CCCAAGCAAG 2097 303 4.96e-09 TGGCTTCGAT TTGTCTCCGGCCGTTTTCGGG ATTGATTTTG 50825 110 6.46e-09 GCTTTTGAGG TTGGTACCGGGCGACGCCTGG ACGGTGTAGT -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 36993 1.4e-10 90_[+3]_389 54681 3.3e-10 146_[+3]_333 47733 1.5e-09 296_[+3]_183 2097 5e-09 302_[+3]_177 50825 6.5e-09 109_[+3]_370 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=21 seqs=5 36993 ( 91) TTTCCAACGGTCGACTACGGG 1 54681 ( 147) TTTGCTGCTGGCGCGGTCGGG 1 47733 ( 297) TCTCCTACTGTCGGGGACGGG 1 2097 ( 303) TTGTCTCCGGCCGTTTTCGGG 1 50825 ( 110) TTGGTACCGGGCGACGCCTGG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 21 n= 7680 bayes= 11.5279 E= 1.5e+003 -897 -897 -897 197 -897 -39 -897 165 -897 -897 86 123 -897 60 86 -35 -897 160 -897 -35 61 -897 -897 123 61 60 -13 -897 -897 193 -897 -897 -897 -897 145 65 -897 -897 218 -897 -897 -39 86 65 -897 193 -897 -897 -897 -897 218 -897 61 -39 -13 -35 -897 60 86 -35 -897 -897 145 65 61 -39 -897 65 -897 193 -897 -897 -897 -897 186 -35 -897 -897 218 -897 -897 -897 218 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 21 nsites= 5 E= 1.5e+003 0.000000 0.000000 0.000000 1.000000 0.000000 0.200000 0.000000 0.800000 0.000000 0.000000 0.400000 0.600000 0.000000 0.400000 0.400000 0.200000 0.000000 0.800000 0.000000 0.200000 0.400000 0.000000 0.000000 0.600000 0.400000 0.400000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.600000 0.400000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.400000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.400000 0.200000 0.200000 0.200000 0.000000 0.400000 0.400000 0.200000 0.000000 0.000000 0.600000 0.400000 0.400000 0.200000 0.000000 0.400000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 1.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- T[TC][TG][CGT][CT][TA][ACG]C[GT]G[GTC]CG[ACGT][CGT][GT][ATC]C[GT]GG -------------------------------------------------------------------------------- Time 6.50 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8694 4.65e-05 152_[+2(1.34e-06)]_145_\ [+1(2.38e-06)]_179 46385 3.08e-02 11_[+1(9.05e-06)]_477 54681 1.07e-07 146_[+3(3.27e-10)]_195_\ [+1(2.00e-05)]_126 15310 6.36e-02 290_[+1(1.19e-05)]_198 54973 4.43e-04 225_[+2(3.68e-07)]_263 44116 2.43e-02 445_[+1(7.39e-06)]_43 50825 8.59e-10 60_[+2(8.32e-07)]_37_[+3(6.46e-09)]_\ 113_[+1(3.59e-06)]_245 11652 1.65e-02 454_[+1(2.00e-05)]_34 34741 1.72e-01 500 34902 7.85e-02 2_[+1(1.50e-05)]_486 3052 2.05e-02 468_[+1(7.39e-06)]_20 35557 9.84e-05 185_[+1(6.72e-05)]_37_\ [+2(1.79e-07)]_254 2097 6.56e-10 129_[+2(1.46e-07)]_161_\ [+3(4.96e-09)]_31_[+1(2.00e-05)]_134 46041 3.56e-04 310_[+1(1.10e-07)]_178 36993 3.96e-08 90_[+3(1.41e-10)]_39_[+1(1.79e-05)]_\ 338 47733 4.08e-06 296_[+3(1.46e-09)]_183 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************