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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/433/433.seqs.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
11242 1.0000 500 11256 1.0000 500
11302 1.0000 500 11357 1.0000 500
14616 1.0000 500 25541 1.0000 500
264575 1.0000 500 4074 1.0000 500
5774 1.0000 500 7623 1.0000 500
8615 1.0000 500 8919 1.0000 500
9282 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/433/433.seqs.fa -oc motifs/433 -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 0.232 G 0.230 T 0.263
Background letter frequencies (from dataset with add-one prior applied):
A 0.275 C 0.232 G 0.230 T 0.263
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MOTIF 1 MEME width = 14 sites = 9 llr = 108 E-value = 1.4e+001
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Motif 1 Description
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Simplified A :79::a::32::12
pos.-specific C ::::7::2111::7
probability G a1:a1:8363::91
matrix T :21:2:24:39a::
bits 2.1 * *
1.9 * * * *
1.7 * * * *
1.5 * * * ***
Relative 1.3 * ** ** ***
Entropy 1.1 * ** ** ***
(17.4 bits) 0.8 * ***** ****
0.6 ******* * ****
0.4 ********* ****
0.2 **************
0.0 --------------
Multilevel GAAGCAGTGGTTGC
consensus T T TGAT A
sequence C A
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Motif 1 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- --------------
264575 114 2.82e-08 TTTAGCGGCA GAAGCAGCGTTTGC TGCCTTTGGT
8919 199 6.84e-08 CCCCGCAGAT GAAGCAGTGGTTGA AGTCAATGCA
5774 185 9.15e-07 TATTGATTTT GAAGTAGGCGTTGC CTCTAGTAAG
9282 393 1.67e-06 TTTGTTTTTC GTAGCATTGCTTGC TATTTGCATT
25541 3 1.98e-06 AC GATGCAGCAATTGC ATCAAACTTT
14616 269 2.65e-06 ACAGGAAGAG GAAGCAGGGTCTGG CTTATGAGAG
8615 394 3.10e-06 ATATTTGAAC GGAGGAGTATTTGC AGCCTCTGTG
7623 258 3.10e-06 TCAATTCATA GTAGCATTGATTGA AATGGCTTCC
4074 84 3.28e-06 AGAAGGAGGC GAAGTAGGAGTTAC CAAAGCCATT
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Motif 1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
264575 2.8e-08 113_[+1]_373
8919 6.8e-08 198_[+1]_288
5774 9.2e-07 184_[+1]_302
9282 1.7e-06 392_[+1]_94
25541 2e-06 2_[+1]_484
14616 2.6e-06 268_[+1]_218
8615 3.1e-06 393_[+1]_93
7623 3.1e-06 257_[+1]_229
4074 3.3e-06 83_[+1]_403
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Motif 1 in BLOCKS format
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BL MOTIF 1 width=14 seqs=9
264575 ( 114) GAAGCAGCGTTTGC 1
8919 ( 199) GAAGCAGTGGTTGA 1
5774 ( 185) GAAGTAGGCGTTGC 1
9282 ( 393) GTAGCATTGCTTGC 1
25541 ( 3) GATGCAGCAATTGC 1
14616 ( 269) GAAGCAGGGTCTGG 1
8615 ( 394) GGAGGAGTATTTGC 1
7623 ( 258) GTAGCATTGATTGA 1
4074 ( 84) GAAGTAGGAGTTAC 1
//
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Motif 1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 14 n= 6331 bayes= 9.59072 E= 1.4e+001
-982 -982 212 -982
128 -982 -105 -24
169 -982 -982 -124
-982 -982 212 -982
-982 152 -105 -24
186 -982 -982 -982
-982 -982 176 -24
-982 -6 54 75
28 -106 127 -982
-31 -106 54 34
-982 -106 -982 175
-982 -982 -982 192
-131 -982 195 -982
-31 152 -105 -982
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Motif 1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 14 nsites= 9 E= 1.4e+001
0.000000 0.000000 1.000000 0.000000
0.666667 0.000000 0.111111 0.222222
0.888889 0.000000 0.000000 0.111111
0.000000 0.000000 1.000000 0.000000
0.000000 0.666667 0.111111 0.222222
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.777778 0.222222
0.000000 0.222222 0.333333 0.444444
0.333333 0.111111 0.555556 0.000000
0.222222 0.111111 0.333333 0.333333
0.000000 0.111111 0.000000 0.888889
0.000000 0.000000 0.000000 1.000000
0.111111 0.000000 0.888889 0.000000
0.222222 0.666667 0.111111 0.000000
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Motif 1 regular expression
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G[AT]AG[CT]A[GT][TGC][GA][GTA]TTG[CA]
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Time 1.56 secs.
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MOTIF 2 MEME width = 16 sites = 9 llr = 115 E-value = 5.4e+001
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Motif 2 Description
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Simplified A :87:1:74:4:6331:
pos.-specific C a::11a31a3a:66:9
probability G :2::4::1:2::1131
matrix T ::393::3:::4::6:
bits 2.1 * * * *
1.9 * * * *
1.7 * * * * *
1.5 * * * * * *
Relative 1.3 * * * * * *
Entropy 1.1 **** ** * * *
(18.4 bits) 0.8 **** ** * ** *
0.6 **** ** * ******
0.4 **** ** ********
0.2 ****************
0.0 ----------------
Multilevel CAATGCAACACACCTC
consensus GT T CT C TAAG
sequence G
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Motif 2 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- ----------------
8919 216 3.31e-09 TGGTTGAAGT CAATGCAACGCACCTC TGAGGAGAAA
11357 145 3.52e-08 TAGGAACCGA CATTTCAACCCTCCTC TTTCCCAACG
264575 172 1.40e-07 GGCCATCAAC CAATTCAACACACCAC ACAGGCGGTC
5774 51 2.92e-07 CAATTACAAG CAATGCCTCCCTGCTC AAAAATTCAT
7623 466 5.95e-07 AAAGCATACG CAATCCAACCCAAAGC TTTAGCGATA
11302 278 1.37e-06 AACGTACCTT CGATGCAGCACTCGTC TTCCTAGGCC
14616 370 2.05e-06 GACCCCTTGA CAATACACCACAAAGC TAATGAGAGG
25541 53 2.33e-06 CTGCATATGG CATTGCCTCGCAACTG AAAAGTGCAG
11242 451 5.37e-06 CAAGAAGCGT CGTCTCCTCACTCAGC ATCAACGCCA
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Motif 2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
8919 3.3e-09 215_[+2]_269
11357 3.5e-08 144_[+2]_340
264575 1.4e-07 171_[+2]_313
5774 2.9e-07 50_[+2]_434
7623 6e-07 465_[+2]_19
11302 1.4e-06 277_[+2]_207
14616 2.1e-06 369_[+2]_115
25541 2.3e-06 52_[+2]_432
11242 5.4e-06 450_[+2]_34
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Motif 2 in BLOCKS format
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BL MOTIF 2 width=16 seqs=9
8919 ( 216) CAATGCAACGCACCTC 1
11357 ( 145) CATTTCAACCCTCCTC 1
264575 ( 172) CAATTCAACACACCAC 1
5774 ( 51) CAATGCCTCCCTGCTC 1
7623 ( 466) CAATCCAACCCAAAGC 1
11302 ( 278) CGATGCAGCACTCGTC 1
14616 ( 370) CAATACACCACAAAGC 1
25541 ( 53) CATTGCCTCGCAACTG 1
11242 ( 451) CGTCTCCTCACTCAGC 1
//
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Motif 2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 16 n= 6305 bayes= 9.58478 E= 5.4e+001
-982 211 -982 -982
150 -982 -5 -982
128 -982 -982 34
-982 -106 -982 175
-131 -106 95 34
-982 211 -982 -982
128 52 -982 -982
69 -106 -105 34
-982 211 -982 -982
69 52 -5 -982
-982 211 -982 -982
101 -982 -982 75
28 126 -105 -982
28 126 -105 -982
-131 -982 54 108
-982 194 -105 -982
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Motif 2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 16 nsites= 9 E= 5.4e+001
0.000000 1.000000 0.000000 0.000000
0.777778 0.000000 0.222222 0.000000
0.666667 0.000000 0.000000 0.333333
0.000000 0.111111 0.000000 0.888889
0.111111 0.111111 0.444444 0.333333
0.000000 1.000000 0.000000 0.000000
0.666667 0.333333 0.000000 0.000000
0.444444 0.111111 0.111111 0.333333
0.000000 1.000000 0.000000 0.000000
0.444444 0.333333 0.222222 0.000000
0.000000 1.000000 0.000000 0.000000
0.555556 0.000000 0.000000 0.444444
0.333333 0.555556 0.111111 0.000000
0.333333 0.555556 0.111111 0.000000
0.111111 0.000000 0.333333 0.555556
0.000000 0.888889 0.111111 0.000000
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Motif 2 regular expression
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C[AG][AT]T[GT]C[AC][AT]C[ACG]C[AT][CA][CA][TG]C
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Time 3.09 secs.
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MOTIF 3 MEME width = 12 sites = 12 llr = 117 E-value = 4.4e+002
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Motif 3 Description
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Simplified A :2::3a2:a:43
pos.-specific C a17a8:38:341
probability G :12:::2::::1
matrix T :72:::42:825
bits 2.1 * *
1.9 * * * *
1.7 * * * *
1.5 * * * **
Relative 1.3 * *** **
Entropy 1.1 * *** ***
(14.0 bits) 0.8 * **** ***
0.6 * **** ***
0.4 ****** ****
0.2 ****** *****
0.0 ------------
Multilevel CTCCCATCATAT
consensus A C CCA
sequence
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Motif 3 sites sorted by position p-value
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Sequence name Start P-value Site
------------- ----- --------- ------------
11357 174 2.91e-07 CCCAACGGCT CTCCCACCATAT GGAACAGAGG
11302 3 8.84e-07 GG CTCCCATCACAT CACCCATCAC
7623 439 1.33e-06 AGGAGAGATA CTGCCATCATCT CATAAAAAGC
9282 283 1.86e-06 GGACTTGTGA CTCCCAACATAA ATGGTGCCAC
8919 92 9.30e-06 TCCCCCCACT CTCCCATCATTC ACAGCAATAA
8615 310 1.29e-05 TTTCTGACAC CTTCAATCATAT CTTTCTCTAG
4074 403 1.68e-05 TGATATAAAC CACCAATCATCA TGACGGATCA
25541 221 2.04e-05 ACAACACATC CTCCAACTATCT CTTAAAACAA
11242 407 4.15e-05 GCAGGTATTT CGGCCACCATCA ACATGAGTAC
14616 420 5.37e-05 AGAAAATTAG CCCCCAACACAA CATCGAGCCC
264575 484 6.88e-05 ACTATCCCAG CACCCAGCACCG CCGCG
5774 106 7.66e-05 TTCCTCATCA CTTCCAGTATTT AGGTCTCTAA
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Motif 3 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
11357 2.9e-07 173_[+3]_315
11302 8.8e-07 2_[+3]_486
7623 1.3e-06 438_[+3]_50
9282 1.9e-06 282_[+3]_206
8919 9.3e-06 91_[+3]_397
8615 1.3e-05 309_[+3]_179
4074 1.7e-05 402_[+3]_86
25541 2e-05 220_[+3]_268
11242 4.1e-05 406_[+3]_82
14616 5.4e-05 419_[+3]_69
264575 6.9e-05 483_[+3]_5
5774 7.7e-05 105_[+3]_383
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Motif 3 in BLOCKS format
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BL MOTIF 3 width=12 seqs=12
11357 ( 174) CTCCCACCATAT 1
11302 ( 3) CTCCCATCACAT 1
7623 ( 439) CTGCCATCATCT 1
9282 ( 283) CTCCCAACATAA 1
8919 ( 92) CTCCCATCATTC 1
8615 ( 310) CTTCAATCATAT 1
4074 ( 403) CACCAATCATCA 1
25541 ( 221) CTCCAACTATCT 1
11242 ( 407) CGGCCACCATCA 1
14616 ( 420) CCCCCAACACAA 1
264575 ( 484) CACCCAGCACCG 1
5774 ( 106) CTTCCAGTATTT 1
//
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Motif 3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 6357 bayes= 9.49463 E= 4.4e+002
-1023 211 -1023 -1023
-72 -147 -146 134
-1023 152 -46 -66
-1023 211 -1023 -1023
-14 169 -1023 -1023
186 -1023 -1023 -1023
-72 11 -46 66
-1023 184 -1023 -66
186 -1023 -1023 -1023
-1023 11 -1023 151
60 85 -1023 -66
28 -147 -146 92
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Motif 3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 12 E= 4.4e+002
0.000000 1.000000 0.000000 0.000000
0.166667 0.083333 0.083333 0.666667
0.000000 0.666667 0.166667 0.166667
0.000000 1.000000 0.000000 0.000000
0.250000 0.750000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.166667 0.250000 0.166667 0.416667
0.000000 0.833333 0.000000 0.166667
1.000000 0.000000 0.000000 0.000000
0.000000 0.250000 0.000000 0.750000
0.416667 0.416667 0.000000 0.166667
0.333333 0.083333 0.083333 0.500000
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Motif 3 regular expression
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CTCC[CA]A[TC]CA[TC][AC][TA]
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Time 4.48 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
------------- ---------------- -------------
11242 1.75e-03 406_[+3(4.15e-05)]_32_\
[+2(5.37e-06)]_34
11256 1.00e+00 500
11302 1.01e-05 2_[+3(8.84e-07)]_[+3(4.45e-05)]_251_\
[+2(1.37e-06)]_207
11357 5.00e-07 144_[+2(3.52e-08)]_13_\
[+3(2.91e-07)]_315
14616 5.54e-06 268_[+1(2.65e-06)]_87_\
[+2(2.05e-06)]_34_[+3(5.37e-05)]_69
25541 2.03e-06 2_[+1(1.98e-06)]_36_[+2(2.33e-06)]_\
152_[+3(2.04e-05)]_268
264575 9.78e-09 113_[+1(2.82e-08)]_44_\
[+2(1.40e-07)]_296_[+3(6.88e-05)]_5
4074 1.62e-04 83_[+1(3.28e-06)]_305_\
[+3(1.68e-05)]_86
5774 5.07e-07 50_[+2(2.92e-07)]_39_[+3(7.66e-05)]_\
67_[+1(9.15e-07)]_16_[+1(8.65e-05)]_272
7623 7.52e-08 257_[+1(3.10e-06)]_167_\
[+3(1.33e-06)]_15_[+2(5.95e-07)]_19
8615 7.28e-04 309_[+3(1.29e-05)]_72_\
[+1(3.10e-06)]_93
8919 1.10e-10 91_[+3(9.30e-06)]_95_[+1(6.84e-08)]_\
3_[+2(3.31e-09)]_269
9282 3.56e-05 282_[+3(1.86e-06)]_98_\
[+1(1.67e-06)]_94
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Stopped because nmotifs = 3 reached.
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CPU: seaotter.hsd1.wa.comcast.net
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