MAST - Motif Alignment and Search Tool
MAST version 3.0 (Release date: 2004/07/16 05:53:30)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.sdsc.edu.
REFERENCE
If you use this program in your research, please cite:
Timothy L. Bailey and Michael Gribskov,
"Combining evidence using p-values: application to sequence homology
searches", Bioinformatics, 14(48-54), 1998.
DATABASE AND MOTIFS
DATABASE /home/meme/meme.3.0.6/tests/crp0.s (nucleotide)
Last updated on Fri Jul 16 15:53:54 2004
Database contains 18 sequences, 1890 residues
Scores for positive and reverse complement strands are combined.
MOTIFS meme.crp0.oops.4.Linuxx86_64.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 15 GTGACCCGGTTCACA
2 11 CGCATAACAAA
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.37
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.281 C 0.222 G 0.229 T 0.267
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 18 sequences has E-value less than 10.
- The E-value of a sequence is the expected number of sequences
in a random database of the same size that would match the motifs as
well as the sequence does and is equal to the combined p-value of the
sequence times the number of sequences in the database.
- The combined p-value of a sequence measures the strength of the
match of the sequence to all the motifs and is calculated by
- finding the score of the single best match of each motif
to the sequence (best matches may overlap),
- calculating the sequence p-value of each score,
- forming the product of the p-values,
- taking the p-value of the product.
- The sequence p-value of a score is defined as the
probability of a random sequence of the same length containing
some match with as good or better a score.
- The score for the match of a position in a sequence to a motif
is computed by by summing the appropriate entry from each column of
the position-dependent scoring matrix that represents the motif.
- Sequences shorter than one or more of the motifs are skipped.
- The table is sorted by increasing E-value.
Links | Sequence Name | Description | E-value | Length
|
---|
| ara
|
| 0.00011
| 105
|
| lac
|
| 0.00027
| 105
|
| malt
|
| 0.00072
| 105
|
| gale
|
| 0.0012
| 105
|
| ompa
|
| 0.0044
| 105
|
| deop2
|
| 0.0052
| 105
|
| male
|
| 0.011
| 105
|
| ilv
|
| 0.012
| 105
|
| tnaa
|
| 0.013
| 105
|
| malk
|
| 0.014
| 105
|
| pbr322
|
| 0.015
| 105
|
| bglr1
|
| 0.026
| 105
|
| cya
|
| 0.029
| 105
|
| crp
|
| 0.034
| 105
|
| trn9cat
|
| 0.056
| 105
|
| tdc
|
| 0.065
| 105
|
| ce1cg
|
| 0.1
| 105
|
| uxu1
|
| 0.19
| 105
|
SECTION II: MOTIF DIAGRAMS
- The ordering and spacing of all non-overlapping motif occurrences
are shown for each high-scoring sequence listed in Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001.
- The POSITION p-value of a match is the probability of
a single random subsequence of the length of the motif
scoring at least as well as the observed match.
- For each sequence, all motif occurrences are shown unless there
are overlaps. In that case, a motif occurrence is shown only if its
p-value is less than the product of the p-values of the other
(lower-numbered) motif occurrences that it overlaps.
- The table also shows the E-value of each sequence.
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
A minus sign indicates that the occurrence is on the
reverse complement strand.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
Links | Name | Expect | Motifs
|
---|
| ara
| 0.00011
|
|
| lac
| 0.00027
|
|
| malt
| 0.00072
|
|
| gale
| 0.0012
|
|
| ompa
| 0.0044
|
|
| deop2
| 0.0052
|
|
| male
| 0.011
|
|
| ilv
| 0.012
|
|
| tnaa
| 0.013
|
|
| malk
| 0.014
|
|
| pbr322
| 0.015
|
|
| bglr1
| 0.026
|
|
| cya
| 0.029
|
|
| crp
| 0.034
|
|
| trn9cat
| 0.056
|
|
| tdc
| 0.065
|
|
| ce1cg
| 0.1
|
|
| uxu1
| 0.19
|
|
SCALE
|
|
---|
SECTION III: ANNOTATED SEQUENCES
- The positions and p-values of the non-overlapping motif occurrences
are shown above the actual sequence for each of the high-scoring
sequences from Section I.
- A motif occurrence is defined as a position in the sequence whose
match to the motif has POSITION p-value less than 0.0001 as
defined in Section II.
- For each sequence, the first line specifies the name of the sequence.
- The second (and possibly more) lines give a description of the
sequence.
- Following the description line(s) is a line giving the length,
combined p-value, and E-value of the sequence as defined in Section I.
- The next line reproduces the motif diagram from Section II.
- The entire sequence is printed on the following lines.
- Motif occurrences are indicated directly above their positions in the
sequence on lines showing
- the motif number of the occurrence (a minus sign indicates that
the occurrence is on the reverse complement strand),
- the position p-value of the occurrence,
- the best possible match to the motif (or its reverse complement), and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
ara
LENGTH = 105 COMBINED P-VALUE = 6.02e-06 E-VALUE = 0.00011
DIAGRAM: 8-[+2]-38-[-1]-2-[-2]-20
[+2] [-1] [
3.0e-06 3.6e-06 8
CGCATAACAAA TGTGAACCGGGTCAC T
+++ +++++++ + ++ ++ +++++++ +
1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACT
-2]
.9e-05
TTGTTATGCG
+++ +++++
76 TTGCTATGCCATAGCATTTTTATCCATAAG
lac
LENGTH = 105 COMBINED P-VALUE = 1.49e-05 E-VALUE = 0.00027
DIAGRAM: 11-[-1]-63-[+2]-5
[-1]
2.1e-06
TGTGAACCGGGTCAC
++++++ +++ ++++
1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG
[+2]
1.4e-05
CGCATAACAAA
++ +++++++
76 TGTGGAATTGTGAGCGGATAACAATTTCAC
malt
LENGTH = 105 COMBINED P-VALUE = 3.99e-05 E-VALUE = 0.00072
DIAGRAM: 44-[+1]-6-[+2]-29
[+1] [+2]
1.5e-05 5.8e-06
GTGACCCGGTTCACA CGCATAACAA
+++++ ++++ ++ + ++++++++++
1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAA
A
+
76 AACGTCATCGCTTGCATTAGAAAGGTTTCT
gale
LENGTH = 105 COMBINED P-VALUE = 6.54e-05 E-VALUE = 0.0012
DIAGRAM: 1-[+2]-42-[+1]-2-[-2]-23
[+2] [+1] [-2]
2.0e-06 7.1e-05 1.7e
CGCATAACAAA GTGACCCGGTTCACA TTTG
+++++++++++ ++ ++ + ++++ ++ ++++
1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTG
-05
TTATGCG
++++++
76 TTATGCTATGGTTATTTCATACCATAAGCC
ompa
LENGTH = 105 COMBINED P-VALUE = 2.44e-04 E-VALUE = 0.0044
DIAGRAM: 51-[+1]-39
[+1]
2.9e-06
GTGACCCGGTTCACA
+++++ ++++++++
1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGT
deop2
LENGTH = 105 COMBINED P-VALUE = 2.86e-04 E-VALUE = 0.0052
DIAGRAM: 9-[-1]-36-[-2]-34
[-1] [-2]
1.2e-05 5.9e-05
TGTGAACCGGGTCAC TTTGTTATGCG
+ +++++++++++ + ++++ +++++
1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATC
male
LENGTH = 105 COMBINED P-VALUE = 6.24e-04 E-VALUE = 0.011
DIAGRAM: 16-[-1]-48-[+2]-15
[-1]
1.9e-05
TGTGAACCGGGTCAC
+++ + + +++++++
1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGG
[+2]
8.9e-05
CGCATAACAAA
++ +++++ ++
76 TTGCCGTATAAAGAAACTAGAGTCCGTTTA
ilv
LENGTH = 105 COMBINED P-VALUE = 6.54e-04 E-VALUE = 0.012
DIAGRAM: 15-[-2]-79
[-2]
9.5e-06
TTTGTTATGCG
++++++++ ++
1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAA
tnaa
LENGTH = 105 COMBINED P-VALUE = 7.08e-04 E-VALUE = 0.013
DIAGRAM: 74-[+1]-16
[
5
G
+
1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTG
+1]
.0e-06
TGACCCGGTTCACA
++++ ++ ++++++
76 TGATTCGATTCACATTTAAACAATTTCAGA
malk
LENGTH = 105 COMBINED P-VALUE = 7.58e-04 E-VALUE = 0.014
DIAGRAM: 64-[+1]-26
[+1]
6.8e-06
GTGACCCGGTT
+++++++ +++
1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT
CACA
++
76 TGCAAAAATCGTGGCGATTTTATGTGCGCA
pbr322
LENGTH = 105 COMBINED P-VALUE = 8.13e-04 E-VALUE = 0.015
DIAGRAM: 55-[-1]-35
[-1]
6.8e-06
TGTGAACCGGGTCAC
++++++++++ +++
1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG
bglr1
LENGTH = 105 COMBINED P-VALUE = 1.47e-03 E-VALUE = 0.026
DIAGRAM: 78-[-1]-12
[-1]
1.2e-05
TGTGAACCGGGTCAC
+++++++ +++++
76 AACTGTGAGCATGGTCATATTTTTATCAAT
cya
LENGTH = 105 COMBINED P-VALUE = 1.59e-03 E-VALUE = 0.029
DIAGRAM: 52-[-1]-38
[-1]
6.2e-06
TGTGAACCGGGTCAC
+++ ++++ ++++++
1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGA
crp
LENGTH = 105 COMBINED P-VALUE = 1.88e-03 E-VALUE = 0.034
DIAGRAM: 65-[-1]-25
[-1]
1.6e-05
TGTGAACCGG
++ ++ ++
1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGAC
GTCAC
+++++
76 GTCACATTACCGTGCAGTACAGTTGATAGC
trn9cat
LENGTH = 105 COMBINED P-VALUE = 3.11e-03 E-VALUE = 0.056
DIAGRAM: 19-[+2]-75
[+2]
3.7e-05
CGCATAACAAA
++++ ++ +++
1 CTGTGACGGAAGATCACTTCGCAGAATAAATAAATCCTGGTGTCCCTGTTGATACCGGGAAGCCCTGGGCCAACT
tdc
LENGTH = 105 COMBINED P-VALUE = 3.62e-03 E-VALUE = 0.065
DIAGRAM: 81-[+1]-9
[+1]
2.3e-05
GTGACCCGGTTCACA
++++ +++ ++++
76 TAATTTGTGAGTGGTCGCACATATCCTGTT
ce1cg
LENGTH = 105 COMBINED P-VALUE = 5.62e-03 E-VALUE = 0.1
DIAGRAM: 64-[+1]-26
[+1]
1.3e-05
GTGACCCGGTT
+++++ +++
1 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTT
CACA
++++
76 CACAAAAATGGAAGTCCACAGTCTTGACAG
uxu1
LENGTH = 105 COMBINED P-VALUE = 1.04e-02 E-VALUE = 0.19
DIAGRAM: 20-[+1]-70
[+1]
1.9e-05
GTGACCCGGTTCACA
+++++++++++ ++
1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAG
Debugging Information
CPU: chromo
Time 0.010000 secs.
mast meme.crp0.oops.4.Linuxx86_64.html -stdout
Button Help
Links to Entrez database at NCBI
Links to sequence scores (section I)
Links to motif diagrams (section II)
Links to sequence/motif annotated alignments (section III)
This information