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.zoops.4.Linuxx86_64.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 19 TGTGAGCGAGGTCACACTT
2 8 CGGCGGGG
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.33
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
|
---|
| male
|
| 0.00048
| 105
|
| ilv
|
| 0.0014
| 105
|
| ara
|
| 0.0014
| 105
|
| ompa
|
| 0.014
| 105
|
| ce1cg
|
| 0.026
| 105
|
| malt
|
| 0.037
| 105
|
| gale
|
| 0.038
| 105
|
| bglr1
|
| 0.046
| 105
|
| crp
|
| 0.054
| 105
|
| deop2
|
| 0.06
| 105
|
| pbr322
|
| 0.075
| 105
|
| cya
|
| 0.077
| 105
|
| tnaa
|
| 0.081
| 105
|
| lac
|
| 0.12
| 105
|
| tdc
|
| 0.24
| 105
|
| uxu1
|
| 0.34
| 105
|
| malk
|
| 0.35
| 105
|
| trn9cat
|
| 0.48
| 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
|
---|
| male
| 0.00048
|
|
| ilv
| 0.0014
|
|
| ara
| 0.0014
|
|
| ompa
| 0.014
|
|
| ce1cg
| 0.026
|
|
| malt
| 0.037
|
|
| gale
| 0.038
|
|
| bglr1
| 0.046
|
|
| crp
| 0.054
|
|
| deop2
| 0.06
|
|
| pbr322
| 0.075
|
|
| cya
| 0.077
|
|
| tnaa
| 0.081
|
|
| lac
| 0.12
|
|
| tdc
| 0.24
|
|
| uxu1
| 0.34
|
|
| malk
| 0.35
|
|
| trn9cat
| 0.48
|
|
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).
male
LENGTH = 105 COMBINED P-VALUE = 2.66e-05 E-VALUE = 0.00048
DIAGRAM: 16-[+1]-5-[+2]-57
[+1] [+2]
3.6e-06 1.5e-05
TGTGAGCGAGGTCACACTT CGGCGGGG
+++ + +++ ++++++++ ++++++++
1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGG
ilv
LENGTH = 105 COMBINED P-VALUE = 7.52e-05 E-VALUE = 0.0014
DIAGRAM: 4-[+2]-29-[+1]-45
[+2] [+1]
7.0e-06 2.4e-05
CGGCGGGG TGTGAGCGAGGTCACACTT
++++++++ ++++++ ++ + ++ ++
1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAA
ara
LENGTH = 105 COMBINED P-VALUE = 7.91e-05 E-VALUE = 0.0014
DIAGRAM: 57-[+1]-29
[+1]
3.6e-08
TGTGAGCGAGGTCACACT
++++ ++++++++++++
1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACT
T
+
76 TTGCTATGCCATAGCATTTTTATCCATAAG
ompa
LENGTH = 105 COMBINED P-VALUE = 7.52e-04 E-VALUE = 0.014
DIAGRAM: 50-[+1]-36
[+1]
4.2e-07
TGTGAGCGAGGTCACACTT
+++ +++++++++++++
1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGT
ce1cg
LENGTH = 105 COMBINED P-VALUE = 1.46e-03 E-VALUE = 0.026
DIAGRAM: 16-[-1]-28-[+1]-23
[-1] [+1]
7.0e-05 1.1e-06
AAGTGTGACCTCGCTCACA TGTGAGCGAGGT
++ ++++ + +++ + + ++++++++ ++
1 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTT
CACACTT
++++ ++
76 CACAAAAATGGAAGTCCACAGTCTTGACAG
malt
LENGTH = 105 COMBINED P-VALUE = 2.08e-03 E-VALUE = 0.037
DIAGRAM: 40-[-1]-46
[-1]
1.3e-06
AAGTGTGACCTCGCTCACA
++ ++++++ + + ++++
1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAA
gale
LENGTH = 105 COMBINED P-VALUE = 2.13e-03 E-VALUE = 0.038
DIAGRAM: 44-[+1]-42
[+1]
1.3e-06
TGTGAGCGAGGTCACACTT
+++ ++ + +++++++++
1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTG
bglr1
LENGTH = 105 COMBINED P-VALUE = 2.57e-03 E-VALUE = 0.046
DIAGRAM: 78-[+1]-8
[+1]
1.6e-06
TGTGAGCGAGGTCACACTT
+++++++ +++++ + ++
76 AACTGTGAGCATGGTCATATTTTTATCAAT
crp
LENGTH = 105 COMBINED P-VALUE = 3.01e-03 E-VALUE = 0.054
DIAGRAM: 65-[+1]-21
[+1]
2.0e-06
TGTGAGCGAG
++ + ++++
1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGAC
GTCACACTT
++++++ ++
76 GTCACATTACCGTGCAGTACAGTTGATAGC
deop2
LENGTH = 105 COMBINED P-VALUE = 3.35e-03 E-VALUE = 0.06
DIAGRAM: 9-[+1]-31-[-1]-27
[+1] [-1]
2.7e-06 8.7e-06
TGTGAGCGAGGTCACACTT AAGTGTGACCTCGCTC
+++++ + ++ ++ ++ ++ ++ +++++ ++ +++
1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATC
ACA
++
76 GAAGTGTGTTGCGGAGTAGATGTTAGAATA
pbr322
LENGTH = 105 COMBINED P-VALUE = 4.16e-03 E-VALUE = 0.075
DIAGRAM: 52-[-1]-34
[-1]
4.7e-06
AAGTGTGACCTCGCTCACA
+++++++ + ++ ++++
1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG
cya
LENGTH = 105 COMBINED P-VALUE = 4.28e-03 E-VALUE = 0.077
DIAGRAM: 49-[-1]-37
[-1]
2.9e-06
AAGTGTGACCTCGCTCACA
+ ++++ ++ + ++++++
1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGA
tnaa
LENGTH = 105 COMBINED P-VALUE = 4.51e-03 E-VALUE = 0.081
DIAGRAM: 73-[+1]-13
[+
5.
TG
++
1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTG
1]
1e-06
TGAGCGAGGTCACACTT
++++ + ++++++ ++
76 TGATTCGATTCACATTTAAACAATTTCAGA
lac
LENGTH = 105 COMBINED P-VALUE = 6.48e-03 E-VALUE = 0.12
DIAGRAM: 11-[+1]-75
[+1]
5.6e-06
TGTGAGCGAGGTCACACTT
++++++ ++ ++++ +++
1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG
tdc
LENGTH = 105 COMBINED P-VALUE = 1.31e-02 E-VALUE = 0.24
DIAGRAM: 78-[+1]-8
[+1]
1.0e-05
TGTGAGCGAGGTCACACTT
++++ + + ++++ +++++
76 TAATTTGTGAGTGGTCGCACATATCCTGTT
uxu1
LENGTH = 105 COMBINED P-VALUE = 1.88e-02 E-VALUE = 0.34
DIAGRAM: 19-[+1]-67
[+1]
1.9e-05
TGTGAGCGAGGTCACACTT
+++++++ ++++ ++ +++
1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAG
malk
LENGTH = 105 COMBINED P-VALUE = 1.94e-02 E-VALUE = 0.35
DIAGRAM: 60-[-1]-26
[-1]
4.2e-05
AAGTGTGACCTCGCT
++ ++++ ++ +++
1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT
CACA
++
76 TGCAAAAATCGTGGCGATTTTATGTGCGCA
trn9cat
LENGTH = 105 COMBINED P-VALUE = 2.64e-02 E-VALUE = 0.48
DIAGRAM: 83-[-1]-3
[-1]
2.4e-05
AAGTGTGACCTCGCTCACA
++ ++ +++++ ++++
76 TTTGGCGAAAATGAGACGTTGATCGGCACG
Debugging Information
CPU: chromo
Time 0.010000 secs.
mast meme.crp0.zoops.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