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 -stdin (nucleotide)
Database contains 4 sequences, 499297 residues
Scores for positive and reverse complement strands are combined.
MOTIFS meme.adh.zoops.4.Linuxx86_64.html (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 27 YSASKFAVRMLTRSMRREYAPHGIRVN
2 25 QGKVVLITGCSSGIGKATAKHLHKE
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1
----- -----
2 0.27
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.070 C 0.024 D 0.040 E 0.052 F 0.040 G 0.074 H 0.029 I 0.041 K 0.052
L 0.096 M 0.017 N 0.032 P 0.065 Q 0.042 R 0.067 S 0.084 T 0.052 V 0.059
W 0.016 Y 0.022
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 4 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 frame of the (best) motif match(es) is shown.
Frames 1, 2, and 3 are labeled a, b c, respectively.
- The table is sorted by increasing E-value.
Links | Sequence Name | Description | Frame | E-value | Length
|
---|
| gb|AE003602.1|AE003602
| Drosophila melanogaster...
| b
| 1.6e-24
| 297266
|
| gb|AE003567.1|AE003567
| Drosophila melanogaster...
| c
| 2.5e-11
| 104808
|
| gb|AE002569.1|AE002569
| Drosophila melanogaster...
| a
| 0.47
| 12850
|
| gb|AE002567.1|AE002567
| Drosophila melanogaster...
| a
| 3.4
| 84373
|
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 SEQUENCE p-value less than 0.0001.
- The SEQUENCE p-value of a match is the probability of
some random subsequence in a set of n,
where n is the sequence length minus the motif width plus 1,
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
in frame f. Frames 1, 2, and 3 are labeled a, b c.
A minus sign indicates that the occurrence is on the
reverse complement strand.
- Sequences longer than 3000 are not shown to scale and are indicated by thicker lines.
Links | Name | Expect | Motifs
|
---|
| gb|AE003602.1|AE003602
| 1.6e-24
|
| +2b
|
| +1b
|
| +2c
|
| +1c
|
| -1b
|
| -2b
|
| -1b
|
| -2b
|
|
|
|
| gb|AE003567.1|AE003567
| 2.5e-11
|
|
| gb|AE002569.1|AE002569
| 0.47
|
|
| gb|AE002567.1|AE002567
| 3.4
|
|
SCALE
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1 |
75 |
150 |
225 |
300 |
375 |
450 |
525 |
600 |
675 |
750 |
825 |
900 |
975 |
1050 |
1125 |
1200 |
1275 |
1350 |
1425 |
1500 |
1575 |
1650 |
1725 |
1800 |
1875 |
1950 |
2025 |
2100 |
2175 |
2250 |
2325 |
2400 |
2475 |
2550 |
2625 |
2700 |
2775 |
2850 |
2925 |
3000 |
3075 |
3150 |
3225 |
3300 |
|
---|
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 SEQUENCE 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/frame 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),
- columns whose match to the motif has a positive score (indicated
by a plus sign), and
- the protein translation of the match (or its reverse).
gi|7296683|gb|AE003602.1|AE003602
Drosophila melanogaster genomic scaffold 142000013386043 section 3 of 8, complete sequence
LENGTH = 297266 COMBINED P-VALUE = 3.95e-25 E-VALUE = 1.6e-24
DIAGRAM: 101659-[+2b]-375-[+1b]-736-[+2c]-375-[+1c]-764-[-1b]-375-[-2b]- 765-[-1b]-375-[-2b]-191218
[+2b]
5.5e-13
Q..G..K..V..V..L..I..T..G..C..
+ + + + + + + + +
A..G..K..V..V..L..I..T..G..A..
101617 CTTGAGATCCCCTTACATAATTCTGGATCGGATCATGAATTTCGCGGGCAAAGTGGTCCTTATTACGGGAGCA
S..S..G..I..G..K..A..T..A..K..H..L..H..K..E..
+ + + + + + + + + + + + +
S..S..G..I..G..A..A..T..A..I..K..F..A..K..Y..
101690 AGCTCCGGAATCGGAGCTGCAACCGCCATTAAGTTTGCCAAGTACGGCGCCTGTCTGGCTCTCAATGGACGCA
[+1b]
1.8e-09
Y..S..A..S..K..F..
+ + +
Y..N..I..S..K..M..
102055 CATCGTGAACGTGTCCAGTGTCAATGGGATTCGCTCCTTCCCTGGCGTTCTGGCCTACAACATATCCAAAATG
A..V..R..M..L..T..R..S..M..R..R..E..Y..A..P..H..G..I..R..V..N..
+ + + + + + + + + + + + + + + + + + +
G..V..D..Q..F..T..R..C..V..A..L..E..L..A..A..K..G..V..R..V..N..
102128 GGAGTGGATCAGTTCACCCGCTGTGTGGCGTTGGAGCTGGCTGCCAAGGGTGTGCGCGTGAACTGCGTGAATC
[+2c
1.7e
Q..G
+ +
S..G
102858 AATGTAGTTTGGATTTTCATTTGAAATTTCGATTCGATGGGCAGCAAGGGCAAGGCTGGTCTGGACTTCTCCG
]
-10
..K..V..V..L..I..T..G..C..S..S..G..I..G..K..A..T..A..K..H..L..H..K..E..
+ + + + + + + + + + + + + + + + + +
..K..V..V..L..I..T..G..A..A..S..G..I..G..A..A..A..A..E..M..F..S..K..L..
102931 GCAAAGTGGTGCTTATCACGGGCGCAGCCTCCGGGATCGGGGCCGCCGCGGCGGAGATGTTCTCGAAGCTGGG
[+1c]
1.2e-14
Y..S..A..S..K..F..A..V..R..M..L..T..R..S..M..R..R..E..Y..A..P..H.
+ + + + + + + + + + + + + + + + + + + + +
Y..N..M..S..K..A..A..V..D..Q..F..T..R..S..L..A..L..D..L..G..P..Q.
103369 TGGTGGCCTACAACATGTCCAAGGCGGCGGTGGACCAGTTTACCCGCTCCCTTGCCCTGGATCTGGGTCCCCA
.G..I..R..V..N..
+ + + + +
.G..V..R..V..N..
103442 GGGTGTTCGGGTGAATGCGGTCAATCCGGGTGTGATTCGCACCAATCTGCAAAAGGCGGGGGGCATGGACGAG
[-1b]
4.1e-13
..N..V..R..I..G..H..P..
+ + + + + + +
..N..V..R..V..G..K..P..
104172 AGTCCACCACGACGCTGCAGCTCGGTGATGATTACGCCGGGATTCACGGAGTTCACACGCACACCCTTGGGAG
A..Y..E..R..R..M..S..R..T..L..M..R..V..A..F..K..S..A..S..Y
+ + + + + + + + + + + + + + + + +
A..L..E..L..A..V..C..R..T..F..Q..D..V..A..A..K..S..V..N..Y
104245 CTAGCTCCAGAGCCACGCACCTGGTGAACTGATCCACGGCAGCCTTGGAAACATTGTATGCTAAGACTCCGGG
[-2b]
2.4e-
..E..
..L..
104610 GCCACTATCTGCTCCGCGGTCTCGTTGAGCTTATCCAAATTCCTGCCCACGATGGTGAGCAGGCCTCCCAGTT
09
K..H..L..H..K..A..T..A..K..G..I..G..S..S..C..G..T..I..L..V..V..K..G..Q
+ + + + + + + + + + + + + + + + + + + +
K..A..L..L..V..S..T..G..A..G..I..G..S..S..A..G..T..V..I..I..V..K..D..K
104683 TAGCCAAGAGCACCGAAGTACCCGCTCCAATTCCCGAACTGGCTCCGGTCACGATTATAACTTTATCCTTGAA
[-1b]
3.7e-11
..N..V..R..I..G..H..P..A..Y..E..R..R..M..
+ + + + + + + + + + + +
..N..V..R..V..G..K..P..A..L..E..L..A..I..
105486 ATGTCAGTCACAATCACGCCGGGATTCACGGCGTTTACGCGGACTCCTTTGGGGGCCAGTTCCAGGGCTATGC
S..R..T..L..M..R..V..A..F..K..S..A..S..Y
+ + + + + + + + + + +
C..A..T..F..Q..D..V..A..A..K..S..V..N..Y
105559 AGGCCGTGAACTGGTCCACCGCTGCCTTAGACACATTGTAGGCCAGGACACCAGGAAAGGCACGCAGTCCACA
[-2b]
8.6e-11
..E..K..H..L..H..K..A..
+ + + + +
..L..K..A..L..H..V..A..
105924 GTCTCCTTCAGCTTCTCCTCGTTGCGACCCACGATGACCAGGAGCCCTCCGAGTTTCGCCAAATGGACGGCGG
T..A..K..G..I..G..S..S..C..G..T..I..L..V..V..K..G..Q
+ + + + + + + + + + + + + + + +
A..S..A..G..I..G..S..S..A..G..T..V..I..I..V..K..D..K
105997 CACTTGCTCCGATGCCGGAGCTGGCGCCGGTAACAATAATCACTTTGTCCTTGAAGGATGACATCGTGGGGTG
gi|7295475|gb|AE003567.1|AE003567
Drosophila melanogaster genomic scaffold 142000013386050 section 54 of 54, complete sequence
LENGTH = 104808 COMBINED P-VALUE = 6.25e-12 E-VALUE = 2.5e-11
DIAGRAM: 87164-[-1c]-17563
[-1c]
2.1e-13
..N..V..R..I..G..H..P..A..Y..E..R..R..M..S..R..T..L..M..R..V..A..F..K..
+ + + + + + + + + + + + + + + + + + + + + +
..N..V..R..I..G..E..P..A..L..D..K..A..A..A..K..T..L..G..I..L..A..T..K..
87163 CAGTTGACGCGAATGCCCTCGGGCGCCAGATCCTTGGCGGCTGCCTTGGTCAAGCCAATCAGCGCGGTCTTGC
S..A..S..Y
+ + +
S..V..S..Y
87236 TGACGGAATAGGCTCCCAGTAGCTATGCGATTAAGATAACGGAGATAAGCATTGAACAACTGAACCGCAGATA
gi|7289065|gb|AE002569.1|AE002569
Drosophila melanogaster genomic scaffold 142000013385354, complete sequence
LENGTH = 12850 COMBINED P-VALUE = 1.17e-01 E-VALUE = 0.47
DIAGRAM: 12850
gi|7289301|gb|AE002567.1|AE002567
Drosophila melanogaster genomic scaffold 142000013385554, complete sequence
LENGTH = 84373 COMBINED P-VALUE = 8.60e-01 E-VALUE = 3.4
DIAGRAM: 84373
Debugging Information
CPU: chromo
Time 1.210000 secs.
mast meme.adh.zoops.4.Linuxx86_64.html -stdin -dna -seqp -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