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.tcm.4.Linuxx86_64.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 19 TGTGAGCGAGGTCACACTT
2 11 GTGGAATTGTT
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.28
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
|
---|
| gale
|
| 1.3e-05
| 105
|
| lac
|
| 5.9e-05
| 105
|
| tnaa
|
| 0.00021
| 105
|
| malt
|
| 0.00027
| 105
|
| ara
|
| 0.00038
| 105
|
| ce1cg
|
| 0.0018
| 105
|
| uxu1
|
| 0.0045
| 105
|
| deop2
|
| 0.015
| 105
|
| ompa
|
| 0.017
| 105
|
| cya
|
| 0.017
| 105
|
| tdc
|
| 0.026
| 105
|
| male
|
| 0.027
| 105
|
| bglr1
|
| 0.032
| 105
|
| crp
|
| 0.045
| 105
|
| pbr322
|
| 0.097
| 105
|
| malk
|
| 0.12
| 105
|
| ilv
|
| 0.22
| 105
|
| trn9cat
|
| 5
| 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
|
---|
| gale
| 1.3e-05
|
|
| lac
| 5.9e-05
|
|
| tnaa
| 0.00021
|
|
| malt
| 0.00027
|
|
| ara
| 0.00038
|
|
| ce1cg
| 0.0018
|
|
| uxu1
| 0.0045
|
|
| deop2
| 0.015
|
|
| ompa
| 0.017
|
|
| cya
| 0.017
|
|
| tdc
| 0.026
|
|
| male
| 0.027
|
|
| bglr1
| 0.032
|
|
| crp
| 0.045
|
|
| pbr322
| 0.097
|
|
| malk
| 0.12
|
|
| ilv
| 0.22
|
|
| trn9cat
| 5
|
|
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).
gale
LENGTH = 105 COMBINED P-VALUE = 6.98e-07 E-VALUE = 1.3e-05
DIAGRAM: 30-[-2]-3-[+1]-42
[-2] [+1]
1.8e-06 6.6e-07
AACAATTCCAC TGTGAGCGAGGTCACACTT
+++++++++++ +++ ++++++++++++++
1 GCGCATAAAAAACGGCTAAATTCTTGTGTAAACGATTCCACTAATTTATTCCATGTCACACTTTTCGCATCTTTG
lac
LENGTH = 105 COMBINED P-VALUE = 3.29e-06 E-VALUE = 5.9e-05
DIAGRAM: 11-[+1]-46-[+2]-7-[-2]
[+1]
9.2e-06
TGTGAGCGAGGTCACACTT
++++++ ++ ++++ +++
1 AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG
[+2] [-2]
1.8e-06 6.6e-07
GTGGAATTGTT AACAATTCCAC
+++++++++++ +++++++++++
76 TGTGGAATTGTGAGCGGATAACAATTTCAC
tnaa
LENGTH = 105 COMBINED P-VALUE = 1.19e-05 E-VALUE = 0.00021
DIAGRAM: 73-[+1]-1-[-2]-1
[+
1.
TG
++
1 TTTTTTAAACATTAAAATTCTTACGTAATTTATAATCTTTAAAAAAAGCATTTAATATTGCTCCCCGAACGATTG
1] [-2]
0e-05 2.4e-06
TGAGCGAGGTCACACTT AACAATTCCAC
++++ + +++++ ++ +++++++++++
76 TGATTCGATTCACATTTAAACAATTTCAGA
malt
LENGTH = 105 COMBINED P-VALUE = 1.49e-05 E-VALUE = 0.00027
DIAGRAM: 40-[-1]-46
[-1]
6.6e-07
AAGTGTGACCTCGCTCACA
++++++++++ + +++++
1 GATCAGCGTCGTTTTAGGTGAGTTGTTAATAAAGATTTGGAATTGTGACACAGTGCAAATTCAGACACATAAAAA
ara
LENGTH = 105 COMBINED P-VALUE = 2.10e-05 E-VALUE = 0.00038
DIAGRAM: 57-[+1]-29
[+1]
2.4e-08
TGTGAGCGAGGTCACACT
+++++ ++ +++++++++
1 GACAAAAACGCGTAACAAAAGTGTCTATAATCACGGCAGAAAAGTCCACATTGATTATTTGCACGGCGTCACACT
T
+
76 TTGCTATGCCATAGCATTTTTATCCATAAG
ce1cg
LENGTH = 105 COMBINED P-VALUE = 1.01e-04 E-VALUE = 0.0018
DIAGRAM: 16-[-1]-28-[+1]-23
[-1] [+1]
5.2e-06 5.3e-07
AAGTGTGACCTCGCTCACA TGTGAGCGAGGT
+++++++ +++++ +++++ ++++++++ + +
1 TAATGTTTGTGCTGGTTTTTGTGGCATCGGGCGAGAATAGCGCGTGGTGTGAAAGACTGTTTTTTTGATCGTTTT
CACACTT
+++++++
76 CACAAAAATGGAAGTCCACAGTCTTGACAG
uxu1
LENGTH = 105 COMBINED P-VALUE = 2.52e-04 E-VALUE = 0.0045
DIAGRAM: 9-[+2]-85
[+2]
6.6e-07
GTGGAATTGTT
+++++++++++
1 CCCATGAGAGTGAAATTGTTGTGATGTGGTTAACCCAATTAGAATTCGGGATTGACATGTCTTACCAAAAGGTAG
deop2
LENGTH = 105 COMBINED P-VALUE = 8.16e-04 E-VALUE = 0.015
DIAGRAM: 9-[+1]-31-[-1]-27
[+1] [-1]
1.9e-06 1.3e-06
TGTGAGCGAGGTCACACTT AAGTGTGACCTCGCTC
+++++ ++++ ++ ++ ++ ++++++++ +++ +++
1 AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATC
ACA
+++
76 GAAGTGTGTTGCGGAGTAGATGTTAGAATA
ompa
LENGTH = 105 COMBINED P-VALUE = 9.18e-04 E-VALUE = 0.017
DIAGRAM: 50-[+1]-36
[+1]
8.3e-07
TGTGAGCGAGGTCACACTT
+ +++ +++ ++++++++
1 GCTGACAAAAAAGATTAAACATACCTTATACAAGACTTTTTTTTCATATGCCTGACGGAGTTCACACTTGTAAGT
cya
LENGTH = 105 COMBINED P-VALUE = 9.34e-04 E-VALUE = 0.017
DIAGRAM: 49-[-1]-37
[-1]
8.5e-06
AAGTGTGACCTCGCTCACA
+ ++++ + ++ +++++++
1 ACGGTGCTACACTTGTATGTAGCGCATCTTTCTTTACGGTCAATCAGCAAGGTGTTAAATTGATCACGTTTTAGA
tdc
LENGTH = 105 COMBINED P-VALUE = 1.46e-03 E-VALUE = 0.026
DIAGRAM: 78-[+1]-8
[+1]
6.7e-06
TGTGAGCGAGGTCACACTT
++++ + + ++++ +++++
76 TAATTTGTGAGTGGTCGCACATATCCTGTT
male
LENGTH = 105 COMBINED P-VALUE = 1.48e-03 E-VALUE = 0.027
DIAGRAM: 16-[+1]-70
[+1]
1.4e-06
TGTGAGCGAGGTCACACTT
+++ + +++ ++++++++
1 ACATTACCGCCAATTCTGTAACAGAGATCACACAAAGCGACGGTGGGGCGTAGGGGCAAGGAGGATGGAAAGAGG
bglr1
LENGTH = 105 COMBINED P-VALUE = 1.79e-03 E-VALUE = 0.032
DIAGRAM: 78-[+1]-8
[+1]
4.0e-06
TGTGAGCGAGGTCACACTT
+++++++ +++++ + ++
76 AACTGTGAGCATGGTCATATTTTTATCAAT
crp
LENGTH = 105 COMBINED P-VALUE = 2.51e-03 E-VALUE = 0.045
DIAGRAM: 65-[+1]-21
[+1]
2.5e-06
TGTGAGCGAG
+++ + +++
1 CACAAAGCGAAAGCTATGCTAAAACAGTCAGGATGCTACAGTAATACATTGATGTACTGCATGTATGCAAAGGAC
GTCACACTT
++++++ ++
76 GTCACATTACCGTGCAGTACAGTTGATAGC
pbr322
LENGTH = 105 COMBINED P-VALUE = 5.41e-03 E-VALUE = 0.097
DIAGRAM: 52-[-1]-34
[-1]
6.7e-06
AAGTGTGACCTCGCTCACA
++++++ ++ ++++++
1 CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG
malk
LENGTH = 105 COMBINED P-VALUE = 6.64e-03 E-VALUE = 0.12
DIAGRAM: 60-[-1]-26
[-1]
2.2e-05
AAGTGTGACCTCGCT
+++ ++++ ++ +++
1 GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT
CACA
+++
76 TGCAAAAATCGTGGCGATTTTATGTGCGCA
ilv
LENGTH = 105 COMBINED P-VALUE = 1.22e-02 E-VALUE = 0.22
DIAGRAM: 41-[+1]-45
[+1]
1.9e-05
TGTGAGCGAGGTCACACTT
+++++++ ++ + +++++
1 GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAA
trn9cat
LENGTH = 105 COMBINED P-VALUE = 2.77e-01 E-VALUE = 5
DIAGRAM: 105
Debugging Information
CPU: chromo
Time 0.010000 secs.
mast meme.crp0.tcm.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