MEME version 4.9.1 (Release date: Fri Aug 23 16:49:42 2013 +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= crp0.s
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
ce1cg 1.0000 105 ara 1.0000 105
bglr1 1.0000 105 crp 1.0000 105
cya 1.0000 105 deop2 1.0000 105
gale 1.0000 105 ilv 1.0000 105
lac 1.0000 105 male 1.0000 105
malk 1.0000 105 malt 1.0000 105
ompa 1.0000 105 tnaa 1.0000 105
uxu1 1.0000 105 pbr322 1.0000 105
trn9cat 1.0000 105 tdc 1.0000 105
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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 crp0.s -oc meme_example_output_files -dna -mod zoops -nmotifs 3 -revcomp
model: mod= zoops nmotifs= 3 evt= inf
object function= E-value of product of p-values
width: minw= 8 maxw= 50 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 2 maxsites= 18 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= 1890 N= 18
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304
Background letter frequencies (from dataset with add-one prior applied):
A 0.304 C 0.196 G 0.196 T 0.304
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MOTIF 1 width = 18 sites = 18 llr = 180 E-value = 1.1e-006
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--------------------------------------------------------------------------------
Motif 1 Description
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Simplified A 662::1181313141183
pos.-specific C ::211::1412212:8:6
probability G 112:9:913512711:21
matrix T 3349:91:21631482:1
bits 2.4
2.1 *
1.9 *
1.6 * *
Relative 1.4 * *
Entropy 1.2 **** **
(14.4 bits) 0.9 ***** * ***
0.7 ***** * ****
0.5 ** ***** * * ****
0.2 ** ******** ******
0.0 ------------------
Multilevel AATTGTGACGTAGATCAC
consensus TTA GACT T GA
sequence G T C
G
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Motif 1 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------------
ara - 59 2.51e-07 TGGCATAGCA AAGTGTGACGCCGTGCAA ATAATCAATG
lac + 9 5.35e-07 AACGCAAT TAATGTGAGTTAGCTCAC TCATTAGGCA
malt + 41 8.61e-07 AAAGATTTGG AATTGTGACACAGTGCAA ATTCAGACAC
ilv - 43 1.69e-06 GCAAAGGGAA AATTGAGGGGTTGATCAC GTTTTGTACT
pbr322 - 57 2.85e-06 CTCCTTACGC ATCTGTGCGGTATTTCAC ACCGCATATG
deop2 + 60 2.85e-06 AGATTTCCTT AATTGTGATGTGTATCGA AGTGTGTTGC
uxu1 + 17 5.17e-06 AGAGTGAAAT TGTTGTGATGTGGTTAAC CCAATTAGAA
trn9cat + 84 5.69e-06 CTTTTGGCGA AAATGAGACGTTGATCGG CACG
ce1cg - 65 7.54e-06 GGACTTCCAT TTTTGTGAAAACGATCAA AAAAACAGTC
ompa + 48 9.04e-06 TTTTTTTCAT ATGCCTGACGGAGTTCAC ACTTGTAAGT
crp - 67 9.89e-06 TACTGCACGG TAATGTGACGTCCTTTGC ATACATGCAG
male + 14 1.29e-05 TTACCGCCAA TTCTGTAACAGAGATCAC ACAAAGCGAC
gale - 46 1.41e-05 AAGATGCGAA AAGTGTGACATGGAATAA ATTAGTGGAA
tdc - 82 1.53e-05 AACAGG ATATGTGCGACCACTCAC AAATTAACTT
malk + 61 1.67e-05 ATGTAAGGAA TTTCGTGATGTTGCTTGC AAAAATCGTG
cya + 50 1.81e-05 TCAATCAGCA AGGTGTTAAATTGATCAC GTTTTAGACC
tnaa + 71 2.73e-05 CTCCCCGAAC GATTGTGATTCGATTCAC ATTTAAACAA
bglr1 + 76 8.30e-05 CAAAGTTAAT AACTGTGAGCATGGTCAT ATTTTTATCA
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Motif 1 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
ara 2.5e-07 58_[-1]_29
lac 5.4e-07 8_[+1]_79
malt 8.6e-07 40_[+1]_47
ilv 1.7e-06 42_[-1]_45
pbr322 2.8e-06 56_[-1]_31
deop2 2.8e-06 59_[+1]_28
uxu1 5.2e-06 16_[+1]_71
trn9cat 5.7e-06 83_[+1]_4
ce1cg 7.5e-06 64_[-1]_23
ompa 9e-06 47_[+1]_40
crp 9.9e-06 66_[-1]_21
male 1.3e-05 13_[+1]_74
gale 1.4e-05 45_[-1]_42
tdc 1.5e-05 81_[-1]_6
malk 1.7e-05 60_[+1]_27
cya 1.8e-05 49_[+1]_38
tnaa 2.7e-05 70_[+1]_17
bglr1 8.3e-05 75_[+1]_12
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Motif 1 in BLOCKS format
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BL MOTIF 1 width=18 seqs=18
ara ( 59) AAGTGTGACGCCGTGCAA 1
lac ( 9) TAATGTGAGTTAGCTCAC 1
malt ( 41) AATTGTGACACAGTGCAA 1
ilv ( 43) AATTGAGGGGTTGATCAC 1
pbr322 ( 57) ATCTGTGCGGTATTTCAC 1
deop2 ( 60) AATTGTGATGTGTATCGA 1
uxu1 ( 17) TGTTGTGATGTGGTTAAC 1
trn9cat ( 84) AAATGAGACGTTGATCGG 1
ce1cg ( 65) TTTTGTGAAAACGATCAA 1
ompa ( 48) ATGCCTGACGGAGTTCAC 1
crp ( 67) TAATGTGACGTCCTTTGC 1
male ( 14) TTCTGTAACAGAGATCAC 1
gale ( 46) AAGTGTGACATGGAATAA 1
tdc ( 82) ATATGTGCGACCACTCAC 1
malk ( 61) TTTCGTGATGTTGCTTGC 1
cya ( 50) AGGTGTTAAATTGATCAC 1
tnaa ( 71) GATTGTGATTCGATTCAC 1
bglr1 ( 76) AACTGTGAGCATGGTCAT 1
//
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Motif 1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 18 n= 1584 bayes= 6.57872 E= 1.1e-006
101 -1081 -182 13
87 -1081 -82 13
-45 -23 18 35
-1081 -82 -1081 155
-1081 -182 227 -1081
-145 -1081 -1081 155
-245 -1081 218 -245
145 -82 -182 -1081
-145 99 50 -45
13 -182 135 -145
-145 18 -82 87
-13 18 18 -13
-145 -182 188 -145
35 -23 -182 35
-245 -1081 -82 145
-245 199 -1081 -87
135 -1081 18 -1081
-13 164 -182 -245
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Motif 1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 18 nsites= 18 E= 1.1e-006
0.611111 0.000000 0.055556 0.333333
0.555556 0.000000 0.111111 0.333333
0.222222 0.166667 0.222222 0.388889
0.000000 0.111111 0.000000 0.888889
0.000000 0.055556 0.944444 0.000000
0.111111 0.000000 0.000000 0.888889
0.055556 0.000000 0.888889 0.055556
0.833333 0.111111 0.055556 0.000000
0.111111 0.388889 0.277778 0.222222
0.333333 0.055556 0.500000 0.111111
0.111111 0.222222 0.111111 0.555556
0.277778 0.222222 0.222222 0.277778
0.111111 0.055556 0.722222 0.111111
0.388889 0.166667 0.055556 0.388889
0.055556 0.000000 0.111111 0.833333
0.055556 0.777778 0.000000 0.166667
0.777778 0.000000 0.222222 0.000000
0.277778 0.611111 0.055556 0.055556
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Motif 1 regular expression
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[AT][AT][TAG]TGTGA[CGT][GA][TC][ATCG]G[AT]TC[AG][CA]
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Time 0.81 secs.
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MOTIF 2 width = 8 sites = 2 llr = 24 E-value = 1.5e+004
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Motif 2 Description
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Simplified A ::::::::
pos.-specific C a::5::::
probability G :aa:aaaa
matrix T :::5::::
bits 2.4 *** ****
2.1 *** ****
1.9 *** ****
1.6 *** ****
Relative 1.4 *** ****
Entropy 1.2 *** ****
(17.5 bits) 0.9 ********
0.7 ********
0.5 ********
0.2 ********
0.0 --------
Multilevel CGGCGGGG
consensus T
sequence
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Motif 2 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- --------
ilv + 5 2.18e-06 GCTC CGGCGGGG TTTTTTGTTA
male + 41 5.56e-06 CACAAAGCGA CGGTGGGG CGTAGGGGCA
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Motif 2 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
ilv 2.2e-06 4_[+2]_93
male 5.6e-06 40_[+2]_57
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Motif 2 in BLOCKS format
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BL MOTIF 2 width=8 seqs=2
ilv ( 5) CGGCGGGG 1
male ( 41) CGGTGGGG 1
//
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Motif 2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 8 n= 1764 bayes= 9.783 E= 1.5e+004
-765 235 -765 -765
-765 -765 235 -765
-765 -765 235 -765
-765 135 -765 71
-765 -765 235 -765
-765 -765 235 -765
-765 -765 235 -765
-765 -765 235 -765
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Motif 2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 8 nsites= 2 E= 1.5e+004
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.500000 0.000000 0.500000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
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Motif 2 regular expression
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CGG[CT]GGGG
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Time 1.34 secs.
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MOTIF 3 width = 11 sites = 2 llr = 31 E-value = 2.0e+004
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Motif 3 Description
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Simplified A :::::::::::
pos.-specific C aa::::::5aa
probability G :::aa5a:5::
matrix T ::a::5:a:::
bits 2.4 ** ** * **
2.1 ** ** * **
1.9 ** ** * **
1.6 ***** ** **
Relative 1.4 ***** *****
Entropy 1.2 ***** *****
(22.3 bits) 0.9 ***********
0.7 ***********
0.5 ***********
0.2 ***********
0.0 -----------
Multilevel CCTGGGGTCCC
consensus T G
sequence
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Motif 3 sites sorted by position p-value
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Sequence name Strand Start P-value Site
------------- ------ ----- --------- -----------
lac - 33 7.89e-08 AAGTGTAAAG CCTGGGGTGCC TAATGAGTGA
trn9cat + 36 2.01e-07 ATAAATAAAT CCTGGTGTCCC TGTTGATACC
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Motif 3 block diagrams
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SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
lac 7.9e-08 32_[-3]_62
trn9cat 2e-07 35_[+3]_59
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Motif 3 in BLOCKS format
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BL MOTIF 3 width=11 seqs=2
lac ( 33) CCTGGGGTGCC 1
trn9cat ( 36) CCTGGTGTCCC 1
//
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Motif 3 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 11 n= 1710 bayes= 9.73809 E= 2.0e+004
-765 235 -765 -765
-765 235 -765 -765
-765 -765 -765 171
-765 -765 235 -765
-765 -765 235 -765
-765 -765 135 71
-765 -765 235 -765
-765 -765 -765 171
-765 135 135 -765
-765 235 -765 -765
-765 235 -765 -765
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Motif 3 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 11 nsites= 2 E= 2.0e+004
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.500000 0.500000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 0.500000 0.500000 0.000000
0.000000 1.000000 0.000000 0.000000
0.000000 1.000000 0.000000 0.000000
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Motif 3 regular expression
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CCTGG[GT]GT[CG]CC
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Time 1.86 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
------------- ---------------- -------------
ce1cg 7.53e-03 64_[-1(7.54e-06)]_23
ara 9.02e-04 58_[-1(2.51e-07)]_29
bglr1 2.01e-01 75_[+1(8.30e-05)]_12
crp 3.77e-02 66_[-1(9.89e-06)]_21
cya 6.49e-02 49_[+1(1.81e-05)]_38
deop2 1.19e-02 59_[+1(2.85e-06)]_28
gale 6.15e-02 45_[-1(1.41e-05)]_42
ilv 4.50e-06 4_[+2(2.18e-06)]_30_[-1(1.69e-06)]_\
45
lac 1.93e-07 8_[+1(5.35e-07)]_6_[-3(7.89e-08)]_\
62
male 1.22e-04 13_[+1(1.29e-05)]_9_[+2(5.56e-06)]_\
57
malk 1.39e-02 60_[+1(1.67e-05)]_27
malt 5.01e-03 40_[+1(8.61e-07)]_47
ompa 3.94e-02 47_[+1(9.04e-06)]_40
tnaa 2.80e-02 74_[-1(1.41e-05)]_13
uxu1 1.70e-02 16_[+1(5.17e-06)]_71
pbr322 6.62e-03 56_[-1(2.85e-06)]_31
trn9cat 5.41e-06 35_[+3(2.01e-07)]_37_[+1(5.69e-06)]_\
4
tdc 6.53e-02 81_[-1(1.53e-05)]_6
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Stopped because nmotifs = 3 reached.
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CPU: tlb-takumi-lt.imb.uq.edu.au
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