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MEME - Motif discovery tool
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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.
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REFERENCE
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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.
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TRAINING SET
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DATAFILE= motifs/432/432.seqs.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
42523 1.0000 500 42736 1.0000 500
9171 1.0000 500 32454 1.0000 500
6732 1.0000 500 46863 1.0000 500
7934 1.0000 500 48747 1.0000 500
49501 1.0000 500 10356 1.0000 500
41496 1.0000 500 10902 1.0000 500
46002 1.0000 500 46567 1.0000 500
34164 1.0000 500 45937 1.0000 500
40338 1.0000 500
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme motifs/432/432.seqs.fa -oc motifs/432 -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= 17 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= 8500 N= 17
strands: +
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.276 C 0.234 G 0.219 T 0.271
Background letter frequencies (from dataset with add-one prior applied):
A 0.276 C 0.234 G 0.219 T 0.271
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MOTIF 1 MEME width = 20 sites = 9 llr = 133 E-value = 3.9e+000
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Motif 1 Description
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Simplified A ::::697::::2:1::389:
pos.-specific C :3:2:1:1::22:3::3::3
probability G 77282:::748131a82216
matrix T 3:8:2:3936:474:21::1
bits 2.2 *
2.0 *
1.8 *
1.5 *
Relative 1.3 * * * * * ** *
Entropy 1.1 **** * **** * ** **
(21.3 bits) 0.9 **** ****** * ** ***
0.7 **** ****** * ** ***
0.4 *********** * ** ***
0.2 ********************
0.0 --------------------
Multilevel GGTGAAATGTGTTTGGAAAG
consensus TCGCG T TGCAGC TCG C
sequence T C G
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Motif 1 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------------------
7934 78 4.93e-10 GGACGTTTTT GGTGAATTGGGTTCGGCGAG CTTACTGTAT
40338 360 3.00e-09 AATTATTTTC GGTGAAATTGGTTTGGTAAC AGTAAACTGT
42523 232 3.51e-08 AAAATTGTTC TGGGAAATGGGATAGGGAAG AACAAACGAA
34164 66 7.60e-08 GGCCGGAATG GCTGGATTGTCCGTGGCAAC GCTGTTCATG
42736 475 9.07e-08 TGGCCAAGTG GGTGTATTTTGATCGTGAAG CGGCAC
32454 302 9.89e-08 TTCCCCATGC TCTGAAATGTCTTGGGAGAG CATGGCATGC
10902 223 3.30e-07 CATTCGTCTC TGTCGAACGTGGGTGGAAAG GCTCCCAAGG
46002 116 3.52e-07 CCCGGCACAA GCGGAAATTGGTTCGTCAGC ACAAAGTATA
46863 31 5.09e-07 TTTAGAGTGC GGTCTCATGTGCGTGGAAAT GTCCGGTATG
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Motif 1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
7934 4.9e-10 77_[+1]_403
40338 3e-09 359_[+1]_121
42523 3.5e-08 231_[+1]_249
34164 7.6e-08 65_[+1]_415
42736 9.1e-08 474_[+1]_6
32454 9.9e-08 301_[+1]_179
10902 3.3e-07 222_[+1]_258
46002 3.5e-07 115_[+1]_365
46863 5.1e-07 30_[+1]_450
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Motif 1 in BLOCKS format
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BL MOTIF 1 width=20 seqs=9
7934 ( 78) GGTGAATTGGGTTCGGCGAG 1
40338 ( 360) GGTGAAATTGGTTTGGTAAC 1
42523 ( 232) TGGGAAATGGGATAGGGAAG 1
34164 ( 66) GCTGGATTGTCCGTGGCAAC 1
42736 ( 475) GGTGTATTTTGATCGTGAAG 1
32454 ( 302) TCTGAAATGTCTTGGGAGAG 1
10902 ( 223) TGTCGAACGTGGGTGGAAAG 1
46002 ( 116) GCGGAAATTGGTTCGTCAGC 1
46863 ( 31) GGTCTCATGTGCGTGGAAAT 1
//
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Motif 1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.96028 E= 3.9e+000
-982 -982 160 30
-982 51 160 -982
-982 -982 2 152
-982 -8 183 -982
101 -982 2 -29
169 -107 -982 -982
127 -982 -982 30
-982 -107 -982 171
-982 -982 160 30
-982 -982 102 104
-982 -8 183 -982
-31 -8 -98 71
-982 -982 60 130
-131 51 -98 71
-982 -982 219 -982
-982 -982 183 -29
27 51 2 -128
150 -982 2 -982
169 -982 -98 -982
-982 51 134 -128
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Motif 1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 20 nsites= 9 E= 3.9e+000
0.000000 0.000000 0.666667 0.333333
0.000000 0.333333 0.666667 0.000000
0.000000 0.000000 0.222222 0.777778
0.000000 0.222222 0.777778 0.000000
0.555556 0.000000 0.222222 0.222222
0.888889 0.111111 0.000000 0.000000
0.666667 0.000000 0.000000 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.666667 0.333333
0.000000 0.000000 0.444444 0.555556
0.000000 0.222222 0.777778 0.000000
0.222222 0.222222 0.111111 0.444444
0.000000 0.000000 0.333333 0.666667
0.111111 0.333333 0.111111 0.444444
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.777778 0.222222
0.333333 0.333333 0.222222 0.111111
0.777778 0.000000 0.222222 0.000000
0.888889 0.000000 0.111111 0.000000
0.000000 0.333333 0.555556 0.111111
--------------------------------------------------------------------------------
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Motif 1 regular expression
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[GT][GC][TG][GC][AGT]A[AT]T[GT][TG][GC][TAC][TG][TC]G[GT][ACG][AG]A[GC]
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Time 2.86 secs.
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MOTIF 2 MEME width = 20 sites = 11 llr = 151 E-value = 4.0e+000
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Motif 2 Description
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Simplified A 164:3:3::11:1::2:321
pos.-specific C :4::1:12:223:::57:5:
probability G 6:2::11:2163:::2:3::
matrix T 3:5a695886159aa13539
bits 2.2
2.0 * **
1.8 * **
1.5 * * *** *
Relative 1.3 * * ** *** *
Entropy 1.1 * * * ** *** * *
(19.8 bits) 0.9 ** * * ** *** * *
0.7 ** *** ** * *** * **
0.4 ****** *************
0.2 ********************
0.0 --------------------
Multilevel GATTTTTTTTGTTTTCCTCT
consensus TCA A A C TAT
sequence G G
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Motif 2 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------------------
46002 264 1.22e-08 CAGCCCGACG TAGTTTTTGTGTTTTCCACT ACCATGGTTC
9171 290 1.75e-08 GACGCTACAA GCTTTTTCTTCGTTTCCACT TGTTTTTCCT
7934 436 6.47e-08 ATCCACGTGA GCTTATTCTTCTTTTGCTCT TGTATAGACA
46567 82 7.89e-08 TAAACAGCAA GCTTATTTTTGTTTTCCGAA ATTGATCACC
49501 79 9.57e-08 TCAAGTACTC GAGTTTTTTGGGTTTGTGCT GATTCTACGA
34164 124 1.66e-07 CTGTAGACCC GAATTTGTGTGGATTCCTCT CCGGTCGGTG
40338 283 2.16e-07 CAAACAAAGG TATTTTATTTATTTTACTTT TTTCCCGAAC
42736 15 2.55e-07 TTCTCGTTCA TCATCTATTCGTTTTCCTTT CTTAGTTTGT
41496 189 3.82e-07 ACTCGTGAAT GAATTTTTTATCTTTACACT GGGATATCAC
10356 263 1.26e-06 ATGGTACGTT GATTTGCTTCGCTTTCTGAT TCCGACAATT
32454 383 1.61e-06 GGGTTACTCA AAATATATTTGCTTTTTTTT TCGACCCGAA
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Motif 2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
46002 1.2e-08 263_[+2]_217
9171 1.8e-08 289_[+2]_191
7934 6.5e-08 435_[+2]_45
46567 7.9e-08 81_[+2]_399
49501 9.6e-08 78_[+2]_402
34164 1.7e-07 123_[+2]_357
40338 2.2e-07 282_[+2]_198
42736 2.6e-07 14_[+2]_466
41496 3.8e-07 188_[+2]_292
10356 1.3e-06 262_[+2]_218
32454 1.6e-06 382_[+2]_98
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Motif 2 in BLOCKS format
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BL MOTIF 2 width=20 seqs=11
46002 ( 264) TAGTTTTTGTGTTTTCCACT 1
9171 ( 290) GCTTTTTCTTCGTTTCCACT 1
7934 ( 436) GCTTATTCTTCTTTTGCTCT 1
46567 ( 82) GCTTATTTTTGTTTTCCGAA 1
49501 ( 79) GAGTTTTTTGGGTTTGTGCT 1
34164 ( 124) GAATTTGTGTGGATTCCTCT 1
40338 ( 283) TATTTTATTTATTTTACTTT 1
42736 ( 15) TCATCTATTCGTTTTCCTTT 1
41496 ( 189) GAATTTTTTATCTTTACACT 1
10356 ( 263) GATTTGCTTCGCTTTCTGAT 1
32454 ( 383) AAATATATTTGCTTTTTTTT 1
//
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Motif 2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 20 n= 8177 bayes= 9.8915 E= 4.0e+000
-160 -1010 154 1
121 63 -1010 -1010
40 -1010 -27 75
-1010 -1010 -1010 188
-1 -136 -1010 123
-1010 -1010 -127 175
-1 -136 -127 101
-1010 -37 -1010 159
-1010 -1010 -27 159
-160 -37 -127 123
-160 -37 154 -157
-1010 22 32 75
-160 -1010 -1010 175
-1010 -1010 -1010 188
-1010 -1010 -1010 188
-60 122 -27 -157
-1010 163 -1010 1
-1 -1010 32 75
-60 122 -1010 1
-160 -1010 -1010 175
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Motif 2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 20 nsites= 11 E= 4.0e+000
0.090909 0.000000 0.636364 0.272727
0.636364 0.363636 0.000000 0.000000
0.363636 0.000000 0.181818 0.454545
0.000000 0.000000 0.000000 1.000000
0.272727 0.090909 0.000000 0.636364
0.000000 0.000000 0.090909 0.909091
0.272727 0.090909 0.090909 0.545455
0.000000 0.181818 0.000000 0.818182
0.000000 0.000000 0.181818 0.818182
0.090909 0.181818 0.090909 0.636364
0.090909 0.181818 0.636364 0.090909
0.000000 0.272727 0.272727 0.454545
0.090909 0.000000 0.000000 0.909091
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.181818 0.545455 0.181818 0.090909
0.000000 0.727273 0.000000 0.272727
0.272727 0.000000 0.272727 0.454545
0.181818 0.545455 0.000000 0.272727
0.090909 0.000000 0.000000 0.909091
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Motif 2 regular expression
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[GT][AC][TA]T[TA]T[TA]TTTG[TCG]TTTC[CT][TAG][CT]T
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Time 5.40 secs.
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MOTIF 3 MEME width = 12 sites = 17 llr = 156 E-value = 5.1e+000
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Motif 3 Description
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Simplified A a36961596947
pos.-specific C :61::9:13152
probability G :131::4:1:1:
matrix T ::::4:1::::1
bits 2.2
2.0
1.8 * *
1.5 * * *
Relative 1.3 * * * * *
Entropy 1.1 * * * * *
(13.2 bits) 0.9 * **** * *
0.7 ************
0.4 ************
0.2 ************
0.0 ------------
Multilevel ACAAACAAAACA
consensus AG T G C A
sequence
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Motif 3 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- ------------
42736 196 1.03e-06 AGCAACGAGC ACAATCGAAACA ACACGCTGTT
46863 297 2.27e-06 AACAATTTTA ACGATCAAAACA GTAGCTGAAA
7934 126 2.90e-06 TGCGTAGAAA ACAAACGAAACC CACGAATGCC
34164 480 5.62e-06 GGGTATCTCG ACAAACAACACC CTCTCCAAA
9171 326 7.18e-06 TCCTACGAGC AGAAACAAAAAA TACTATGTGG
42523 325 9.02e-06 GGCGCGTCGC ACAGACAAAAAA CGATCCTTGC
10356 312 1.28e-05 GCTTTGGTAA AAAATCAACAAA ATGGACACCG
49501 245 1.28e-05 TTAGGATATG ACGGACGAAACA TGAATTCGTG
41496 478 2.45e-05 GTCAATTTTT ACAAAAGAAACA CTCACGGCAC
32454 158 2.45e-05 AATTCTAGAT AAAATCGAGACA AATCTAGTGT
6732 177 3.21e-05 CGCCACTTCC ACAATCAACAAT TCAAATGAAG
10902 130 4.01e-05 GCTACCGACA AAGAACAACAAC TGGATGCTGC
45937 149 4.39e-05 GTTGTTATTG AAGAACACAAAA CGACGATGGA
48747 384 4.39e-05 AAAATTGTGG AAAAACTACACA CACTCCCTTT
40338 456 8.27e-05 TTGTAGCACA AGGAACGCAAAA AAGGCTCCTT
46567 205 1.27e-04 ATTGCCAGAC ACAATCGAACCT AAACCCAAAG
46002 429 1.95e-04 ACGCTGTGAA ACCAACAAGAGA CACGCAGTAG
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Motif 3 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
42736 1e-06 195_[+3]_293
46863 2.3e-06 296_[+3]_192
7934 2.9e-06 125_[+3]_363
34164 5.6e-06 479_[+3]_9
9171 7.2e-06 325_[+3]_163
42523 9e-06 324_[+3]_164
10356 1.3e-05 311_[+3]_177
49501 1.3e-05 244_[+3]_244
41496 2.4e-05 477_[+3]_11
32454 2.4e-05 157_[+3]_331
6732 3.2e-05 176_[+3]_312
10902 4e-05 129_[+3]_359
45937 4.4e-05 148_[+3]_340
48747 4.4e-05 383_[+3]_105
40338 8.3e-05 455_[+3]_33
46567 0.00013 204_[+3]_284
46002 0.00019 428_[+3]_60
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Motif 3 in BLOCKS format
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BL MOTIF 3 width=12 seqs=17
42736 ( 196) ACAATCGAAACA 1
46863 ( 297) ACGATCAAAACA 1
7934 ( 126) ACAAACGAAACC 1
34164 ( 480) ACAAACAACACC 1
9171 ( 326) AGAAACAAAAAA 1
42523 ( 325) ACAGACAAAAAA 1
10356 ( 312) AAAATCAACAAA 1
49501 ( 245) ACGGACGAAACA 1
41496 ( 478) ACAAAAGAAACA 1
32454 ( 158) AAAATCGAGACA 1
6732 ( 177) ACAATCAACAAT 1
10902 ( 130) AAGAACAACAAC 1
45937 ( 149) AAGAACACAAAA 1
48747 ( 384) AAAAACTACACA 1
40338 ( 456) AGGAACGCAAAA 1
46567 ( 205) ACAATCGAACCT 1
46002 ( 429) ACCAACAAGAGA 1
//
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Motif 3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 8313 bayes= 8.93074 E= 5.1e+000
186 -1073 -1073 -1073
9 133 -90 -1073
123 -199 42 -1073
168 -1073 -90 -1073
123 -1073 -1073 38
-222 201 -1073 -1073
94 -1073 91 -220
168 -99 -1073 -1073
109 33 -90 -1073
177 -199 -1073 -1073
58 118 -190 -1073
136 -41 -1073 -120
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Motif 3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 17 E= 5.1e+000
1.000000 0.000000 0.000000 0.000000
0.294118 0.588235 0.117647 0.000000
0.647059 0.058824 0.294118 0.000000
0.882353 0.000000 0.117647 0.000000
0.647059 0.000000 0.000000 0.352941
0.058824 0.941176 0.000000 0.000000
0.529412 0.000000 0.411765 0.058824
0.882353 0.117647 0.000000 0.000000
0.588235 0.294118 0.117647 0.000000
0.941176 0.058824 0.000000 0.000000
0.411765 0.529412 0.058824 0.000000
0.705882 0.176471 0.000000 0.117647
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Motif 3 regular expression
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A[CA][AG]A[AT]C[AG]A[AC]A[CA]A
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Time 7.96 secs.
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SUMMARY OF MOTIFS
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Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
42523 8.28e-06 231_[+1(3.51e-08)]_1_[+3(3.72e-05)]_\
60_[+3(9.02e-06)]_164
42736 1.03e-09 14_[+2(2.55e-07)]_161_\
[+3(1.03e-06)]_267_[+1(9.07e-08)]_6
9171 1.55e-06 289_[+2(1.75e-08)]_16_\
[+3(7.18e-06)]_163
32454 1.12e-07 157_[+3(2.45e-05)]_132_\
[+1(9.89e-08)]_61_[+2(1.61e-06)]_98
6732 1.40e-01 176_[+3(3.21e-05)]_312
46863 3.37e-06 30_[+1(5.09e-07)]_246_\
[+3(2.27e-06)]_123_[+3(5.45e-05)]_57
7934 5.77e-12 3_[+3(2.25e-05)]_62_[+1(4.93e-10)]_\
28_[+3(2.90e-06)]_298_[+2(6.47e-08)]_45
48747 7.08e-02 383_[+3(4.39e-05)]_105
49501 3.55e-05 78_[+2(9.57e-08)]_146_\
[+3(1.28e-05)]_178_[+2(6.83e-05)]_46
10356 5.52e-05 262_[+2(1.26e-06)]_29_\
[+3(1.28e-05)]_177
41496 1.94e-04 188_[+2(3.82e-07)]_269_\
[+3(2.45e-05)]_11
10902 6.56e-05 129_[+3(4.01e-05)]_81_\
[+1(3.30e-07)]_258
46002 2.63e-08 115_[+1(3.52e-07)]_128_\
[+2(1.22e-08)]_217
46567 3.46e-05 81_[+2(7.89e-08)]_399
34164 2.83e-09 65_[+1(7.60e-08)]_38_[+2(1.66e-07)]_\
336_[+3(5.62e-06)]_9
45937 1.36e-02 148_[+3(4.39e-05)]_340
40338 2.14e-09 282_[+2(2.16e-07)]_57_\
[+1(3.00e-09)]_76_[+3(8.27e-05)]_33
--------------------------------------------------------------------------------
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Stopped because nmotifs = 3 reached.
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CPU: seaotter.hsd1.wa.comcast.net
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