******************************************************************************** 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/469/469.seqs.fa ALPHABET= ACGT Sequence name Weight Length Sequence name Weight Length ------------- ------ ------ ------------- ------ ------ 8524 1.0000 500 47785 1.0000 500 48345 1.0000 500 49275 1.0000 500 54178 1.0000 500 16940 1.0000 500 4823 1.0000 500 11401 1.0000 500 8537 1.0000 500 43410 1.0000 500 36444 1.0000 500 39554 1.0000 500 47260 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/469/469.seqs.fa -oc motifs/469 -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= 13 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= 6500 N= 13 strands: + sample: seed= 0 seqfrac= 1 Letter frequencies in dataset: A 0.275 C 0.247 G 0.222 T 0.257 Background letter frequencies (from dataset with add-one prior applied): A 0.275 C 0.247 G 0.222 T 0.257 ******************************************************************************** ******************************************************************************** MOTIF 1 MEME width = 12 sites = 10 llr = 107 E-value = 3.3e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 1 Description -------------------------------------------------------------------------------- Simplified A :7::2::638:: pos.-specific C 137a:9:1::7a probability G 9:3::193512: matrix T ::::8:1:211: bits 2.2 2.0 * * 1.7 * * * * 1.5 * * ** * Relative 1.3 * **** * Entropy 1.1 ******* * * (15.5 bits) 0.9 ******* *** 0.7 ************ 0.4 ************ 0.2 ************ 0.0 ------------ Multilevel GACCTCGAGACC consensus CG A GA G sequence T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ------------ 11401 257 5.03e-07 CCGACGGACC GACCTCGGAACC TACGCTTGCC 8524 455 7.74e-07 CCGGTGATCC GACCTCGGTACC TACTGGGTCC 8537 288 1.45e-06 CAAAACTGTG GACCTCGAGTCC GTGACATCCT 49275 169 2.38e-06 GAATTGGAAG GCCCTCGCGACC GTCCCAACAA 47785 275 2.67e-06 TGCGAGGTCT GCCCTCGAGGCC ATTGAAATGC 4823 42 3.72e-06 GTCTACGTTG GAGCTGGAGACC TGCACACACT 16940 347 6.38e-06 AGGTATGTAT GCGCTCGAAAGC ACAAAATTCT 39554 396 1.24e-05 ACATCAATCT GAGCACGAAAGC TCCTTTCACG 48345 19 1.75e-05 CACAGATGAT GACCACGATATC CACATTAATG 47260 410 2.66e-05 GTGGAAATCC CACCTCTGGACC GTCTCATCAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11401 5e-07 256_[+1]_232 8524 7.7e-07 454_[+1]_34 8537 1.4e-06 287_[+1]_201 49275 2.4e-06 168_[+1]_320 47785 2.7e-06 274_[+1]_214 4823 3.7e-06 41_[+1]_447 16940 6.4e-06 346_[+1]_142 39554 1.2e-05 395_[+1]_93 48345 1.8e-05 18_[+1]_470 47260 2.7e-05 409_[+1]_79 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 1 width=12 seqs=10 11401 ( 257) GACCTCGGAACC 1 8524 ( 455) GACCTCGGTACC 1 8537 ( 288) GACCTCGAGTCC 1 49275 ( 169) GCCCTCGCGACC 1 47785 ( 275) GCCCTCGAGGCC 1 4823 ( 42) GAGCTGGAGACC 1 16940 ( 347) GCGCTCGAAAGC 1 39554 ( 396) GAGCACGAAAGC 1 48345 ( 19) GACCACGATATC 1 47260 ( 410) CACCTCTGGACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.56183 E= 3.3e+001 -997 -130 202 -997 135 28 -997 -997 -997 150 44 -997 -997 202 -997 -997 -46 -997 -997 164 -997 187 -115 -997 -997 -997 202 -136 113 -130 44 -997 13 -997 117 -36 154 -997 -115 -136 -997 150 -15 -136 -997 202 -997 -997 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 12 nsites= 10 E= 3.3e+001 0.000000 0.100000 0.900000 0.000000 0.700000 0.300000 0.000000 0.000000 0.000000 0.700000 0.300000 0.000000 0.000000 1.000000 0.000000 0.000000 0.200000 0.000000 0.000000 0.800000 0.000000 0.900000 0.100000 0.000000 0.000000 0.000000 0.900000 0.100000 0.600000 0.100000 0.300000 0.000000 0.300000 0.000000 0.500000 0.200000 0.800000 0.000000 0.100000 0.100000 0.000000 0.700000 0.200000 0.100000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 1 regular expression -------------------------------------------------------------------------------- G[AC][CG]C[TA]CG[AG][GAT]A[CG]C -------------------------------------------------------------------------------- Time 1.49 secs. ******************************************************************************** ******************************************************************************** MOTIF 2 MEME width = 15 sites = 9 llr = 111 E-value = 5.5e+001 ******************************************************************************** -------------------------------------------------------------------------------- Motif 2 Description -------------------------------------------------------------------------------- Simplified A :1:::62111:::9: pos.-specific C ::12:47:3::791: probability G :231a:1811a31:7 matrix T a767:::148::::3 bits 2.2 * * 2.0 * * * 1.7 * * * 1.5 * * * * Relative 1.3 * * * ** Entropy 1.1 * * * ****** (17.9 bits) 0.9 ** ***** ****** 0.7 ******** ****** 0.4 ******** ****** 0.2 *************** 0.0 --------------- Multilevel TTTTGACGTTGCCAG consensus GGC CA C G T sequence -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- --------------- 11401 379 6.89e-09 GGCAAGCCCG TTGTGCCGCTGCCAG AAGGGAGCCC 48345 257 1.50e-07 GTGGTCGAGA TTGTGACTTTGCCAG ATTTCGACGC 36444 137 1.86e-07 CTTAAAAAAT TGTTGAGGTTGCCAG AGATAAGTAC 4823 360 6.35e-07 AGATAAGCTT TTTGGACGTAGCCAG GAGAGTAAGA 49275 335 9.15e-07 TAAATATTTG TTTCGAAGCTGGCAT CATCTGGGAA 8524 164 1.00e-06 CTGACGACAA TTGTGCCATTGGCAT CGAACAATGC 16940 253 3.39e-06 TAGCTTTTGA TGTTGCAGCTGCCCT TTCTTACCTG 8537 314 4.12e-06 CATCCTTGGA TATTGACGAGGGCAG CACTCCCGAA 54178 394 4.68e-06 CTATGACTTT TTCCGCCGGTGCGAG CGTCTTCATC -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11401 6.9e-09 378_[+2]_107 48345 1.5e-07 256_[+2]_229 36444 1.9e-07 136_[+2]_349 4823 6.3e-07 359_[+2]_126 49275 9.1e-07 334_[+2]_151 8524 1e-06 163_[+2]_322 16940 3.4e-06 252_[+2]_233 8537 4.1e-06 313_[+2]_172 54178 4.7e-06 393_[+2]_92 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 2 width=15 seqs=9 11401 ( 379) TTGTGCCGCTGCCAG 1 48345 ( 257) TTGTGACTTTGCCAG 1 36444 ( 137) TGTTGAGGTTGCCAG 1 4823 ( 360) TTTGGACGTAGCCAG 1 49275 ( 335) TTTCGAAGCTGGCAT 1 8524 ( 164) TTGTGCCATTGGCAT 1 16940 ( 253) TGTTGCAGCTGCCCT 1 8537 ( 314) TATTGACGAGGGCAG 1 54178 ( 394) TTCCGCCGGTGCGAG 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 15 n= 6318 bayes= 9.58775 E= 5.5e+001 -982 -982 -982 196 -130 -982 0 138 -982 -115 59 111 -982 -15 -99 138 -982 -982 217 -982 101 85 -982 -982 -31 143 -99 -982 -130 -982 181 -121 -130 43 -99 79 -130 -982 -99 160 -982 -982 217 -982 -982 143 59 -982 -982 185 -99 -982 169 -115 -982 -982 -982 -982 159 38 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 15 nsites= 9 E= 5.5e+001 0.000000 0.000000 0.000000 1.000000 0.111111 0.000000 0.222222 0.666667 0.000000 0.111111 0.333333 0.555556 0.000000 0.222222 0.111111 0.666667 0.000000 0.000000 1.000000 0.000000 0.555556 0.444444 0.000000 0.000000 0.222222 0.666667 0.111111 0.000000 0.111111 0.000000 0.777778 0.111111 0.111111 0.333333 0.111111 0.444444 0.111111 0.000000 0.111111 0.777778 0.000000 0.000000 1.000000 0.000000 0.000000 0.666667 0.333333 0.000000 0.000000 0.888889 0.111111 0.000000 0.888889 0.111111 0.000000 0.000000 0.000000 0.000000 0.666667 0.333333 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 2 regular expression -------------------------------------------------------------------------------- T[TG][TG][TC]G[AC][CA]G[TC]TG[CG]CA[GT] -------------------------------------------------------------------------------- Time 2.94 secs. ******************************************************************************** ******************************************************************************** MOTIF 3 MEME width = 16 sites = 5 llr = 80 E-value = 1.6e+002 ******************************************************************************** -------------------------------------------------------------------------------- Motif 3 Description -------------------------------------------------------------------------------- Simplified A 2a2::8:::2:::8:: pos.-specific C ::8a:::4642:::8a probability G 8:::a2a::22a8:2: matrix T :::::::6426:22:: bits 2.2 * * * 2.0 * ** * * * 1.7 * ** * * * 1.5 * ** * * * Relative 1.3 ******* ** ** Entropy 1.1 ********* ***** (22.9 bits) 0.9 ********* ***** 0.7 ********* ****** 0.4 ********* ****** 0.2 ********* ****** 0.0 ---------------- Multilevel GACCGAGTCCTGGACC consensus A A G CTAC TTG sequence GG T -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 sites sorted by position p-value -------------------------------------------------------------------------------- Sequence name Start P-value Site ------------- ----- --------- ---------------- 11401 484 1.48e-09 GTGTCCTCAG GACCGAGTCCGGGACC A 47260 370 1.07e-08 CCGTCGACTG GACCGAGTCTTGGTCC AAGCAAAGCT 8537 118 4.62e-08 CCTGGTGGTG GACCGGGCCACGGACC TGGAGGAGCG 48345 328 8.28e-08 CACCATCGAC GAACGAGTTGTGGAGC AATTGCATGA 8524 331 8.28e-08 CCGTCGCGTA AACCGAGCTCTGTACC CAGTAATGAG -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 block diagrams -------------------------------------------------------------------------------- SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 11401 1.5e-09 483_[+3]_1 47260 1.1e-08 369_[+3]_115 8537 4.6e-08 117_[+3]_367 48345 8.3e-08 327_[+3]_157 8524 8.3e-08 330_[+3]_154 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 in BLOCKS format -------------------------------------------------------------------------------- BL MOTIF 3 width=16 seqs=5 11401 ( 484) GACCGAGTCCGGGACC 1 47260 ( 370) GACCGAGTCTTGGTCC 1 8537 ( 118) GACCGGGCCACGGACC 1 48345 ( 328) GAACGAGTTGTGGAGC 1 8524 ( 331) AACCGAGCTCTGTACC 1 // -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific scoring matrix -------------------------------------------------------------------------------- log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 9.73306 E= 1.6e+002 -46 -897 185 -897 186 -897 -897 -897 -46 169 -897 -897 -897 202 -897 -897 -897 -897 217 -897 154 -897 -15 -897 -897 -897 217 -897 -897 70 -897 122 -897 128 -897 64 -46 70 -15 -36 -897 -30 -15 122 -897 -897 217 -897 -897 -897 185 -36 154 -897 -897 -36 -897 169 -15 -897 -897 202 -897 -897 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 position-specific probability matrix -------------------------------------------------------------------------------- letter-probability matrix: alength= 4 w= 16 nsites= 5 E= 1.6e+002 0.200000 0.000000 0.800000 0.000000 1.000000 0.000000 0.000000 0.000000 0.200000 0.800000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.000000 1.000000 0.000000 0.800000 0.000000 0.200000 0.000000 0.000000 0.000000 1.000000 0.000000 0.000000 0.400000 0.000000 0.600000 0.000000 0.600000 0.000000 0.400000 0.200000 0.400000 0.200000 0.200000 0.000000 0.200000 0.200000 0.600000 0.000000 0.000000 1.000000 0.000000 0.000000 0.000000 0.800000 0.200000 0.800000 0.000000 0.000000 0.200000 0.000000 0.800000 0.200000 0.000000 0.000000 1.000000 0.000000 0.000000 -------------------------------------------------------------------------------- -------------------------------------------------------------------------------- Motif 3 regular expression -------------------------------------------------------------------------------- [GA]A[CA]CG[AG]G[TC][CT][CAGT][TCG]G[GT][AT][CG]C -------------------------------------------------------------------------------- Time 4.33 secs. ******************************************************************************** ******************************************************************************** SUMMARY OF MOTIFS ******************************************************************************** -------------------------------------------------------------------------------- Combined block diagrams: non-overlapping sites with p-value < 0.0001 -------------------------------------------------------------------------------- SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM ------------- ---------------- ------------- 8524 2.63e-09 163_[+2(1.00e-06)]_152_\ [+3(8.28e-08)]_108_[+1(7.74e-07)]_34 47785 1.58e-02 274_[+1(2.67e-06)]_214 48345 8.07e-09 18_[+1(1.75e-05)]_226_\ [+2(1.50e-07)]_56_[+3(8.28e-08)]_157 49275 9.90e-06 168_[+1(2.38e-06)]_154_\ [+2(9.15e-07)]_151 54178 4.05e-02 393_[+2(4.68e-06)]_92 16940 3.20e-04 174_[+2(6.28e-05)]_63_\ [+2(3.39e-06)]_79_[+1(6.38e-06)]_142 4823 2.09e-05 41_[+1(3.72e-06)]_306_\ [+2(6.35e-07)]_126 11401 3.84e-13 82_[+1(1.48e-05)]_162_\ [+1(5.03e-07)]_110_[+2(6.89e-09)]_41_[+3(7.42e-05)]_33_[+3(1.48e-09)]_1 8537 1.01e-08 117_[+3(4.62e-08)]_154_\ [+1(1.45e-06)]_14_[+2(4.12e-06)]_172 43410 8.16e-01 500 36444 1.80e-03 136_[+2(1.86e-07)]_349 39554 1.07e-02 395_[+1(1.24e-05)]_93 47260 5.12e-06 369_[+3(1.07e-08)]_24_\ [+1(2.66e-05)]_79 -------------------------------------------------------------------------------- ******************************************************************************** ******************************************************************************** Stopped because nmotifs = 3 reached. ******************************************************************************** CPU: seaotter.hsd1.wa.comcast.net ********************************************************************************