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/INO_up800.s (nucleotide)
Last updated on Fri Jul 16 15:53:51 2004
Database contains 7 sequences, 5600 residues
Scores for positive and reverse complement strands are combined.
MOTIFS meme.INO_up800.tcm.4.Linuxx86_64.html (nucleotide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 15 TTCACATGCCGCCCC
2 21 GGCCACATCGCCACTGGCGGC
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 0.281 C 0.222 G 0.229 T 0.267
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 7 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
|
---|
| INO1
| sequence of the region up...
| 4.4e-09
| 800
|
| FAS2
| sequence of the region up...
| 5.2e-07
| 800
|
| FAS1
| sequence of the region up...
| 1.1e-06
| 800
|
| OPI3
| sequence of the region up...
| 1.5e-05
| 800
|
| ACC1
| sequence of the region up...
| 5.8e-05
| 800
|
| CHO1
| sequence of the region up...
| 0.023
| 800
|
| CHO2
| sequence of the region up...
| 0.094
| 800
|
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
|
---|
| INO1
| 4.4e-09
|
|
| FAS2
| 5.2e-07
|
|
| FAS1
| 1.1e-06
|
|
| OPI3
| 1.5e-05
|
|
| ACC1
| 5.8e-05
|
|
| CHO1
| 0.023
|
|
| CHO2
| 0.094
|
|
SCALE
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1 |
25 |
50 |
75 |
100 |
125 |
150 |
175 |
200 |
225 |
250 |
275 |
300 |
325 |
350 |
375 |
400 |
425 |
450 |
475 |
500 |
525 |
550 |
575 |
600 |
625 |
650 |
675 |
700 |
725 |
750 |
775 |
|
---|
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).
INO1
sequence of the region upstream from YJL153C
LENGTH = 800 COMBINED P-VALUE = 6.30e-10 E-VALUE = 4.4e-09
DIAGRAM: 365-[-2]-160-[-1]-6-[-1]-34-[-1]-55-[+1]-4-[+2]-74
[-2]
1.5e-10
GCCGCCAGTG
++++++++++
301 GTGACCTGGAAGCTCACCCTGCAGAGGAATCTCAAGCACAGCCTCCAGCATATGATGAAGACGATGAGGCCGGTG
GCGATGTGGCC
+++++++++++
376 CCGATGTGCCCTTGATGGACAACAAACAACAGCTCTCTTCCGGCCGTACTTAGTGATCGGAACGAGCTCTTTATC
[-1] [-1]
5.3e-06 1.7e-06
GGGGCGGCATGTGAA GGGGCGGCATGTGAA
+++++++ +++ + + +++++++ +++++++
526 TGAAATACGTGCCGGTGTTCCGGGGTTGGATGCGGAATCGAAAGTGTTGAATGTGAAATATGCGGAGGCCAAGTA
[-1]
6.6e-08
GGGGCGGCATGTGAA
+++++++++++++++
601 TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG
[+1] [+2]
2.1e-06 2.1e-07
TTCACATGCCGCCCC GGCCACATCGCCACTGGCGGC
+++++++++++++ + ++++ ++ ++ +++++++
676 AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTAATTTGAGACGTATATAA
FAS2
sequence of the region upstream from YPL231W
LENGTH = 800 COMBINED P-VALUE = 7.49e-08 E-VALUE = 5.2e-07
DIAGRAM: 566-[+1]-131-[+2]-67
[+1]
4.0e-07
TTCACATGCCGCCCC
+++++++++ +++++
526 GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCATTCGCCTCGTAACGTTAC
[+2]
3.7e-09
GGCCACATCGCCACTGGCGGC
+ +++++++++++++++++++
676 TGCCTCATATATAACTTGTTAACTGAAGGTTACACAAGACCACATCACCACTGTCGTGCTTTTCTAATAACCGCT
FAS1
sequence of the region upstream from YKL182W
LENGTH = 800 COMBINED P-VALUE = 1.51e-07 E-VALUE = 1.1e-06
DIAGRAM: 52-[+2]-21-[+1]-691
[+2]
1.8e-07
GGCCACATCGCCACTGGCGGC
+ ++++ + ++ ++++++++
1 CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCACTACTCCCCTGGCCTCCA
[+1]
1.7e-08
TTCACATGCCGCCCC
++++++++++++++
76 ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCGATCTTTCCGTCGCACAA
OPI3
sequence of the region upstream from YJR073C
LENGTH = 800 COMBINED P-VALUE = 2.07e-06 E-VALUE = 1.5e-05
DIAGRAM: 291-[+2]-41-[-2]-126-[-2]-60-[-1]-40-[+1]-149
[+2]
9.1e-07
GGCCACATC
+ +++ +++
226 ATAACGAGTCCGGTGAACTTGGTTCCTTGCTGAACAGTGTCTTCTTGTAAAGCTTCCCATTTGGTGGTCCCGTTC
[-2]
1.7e-06
GCCACTGGCGGC GCCGCCAGTGGCGATGTGGCC
+++ +++++ ++ + +++++++ ++ +++ + +
301 AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGACCGTCTCCAAGAGATCC
[-2]
2.5e-08
GCCGCCAGTGGCGATGTGGCC
+++++++++ +++++++ +++
451 TGTGTATCGGGGACTTCTCTTAGAGTAGAAGCGTCTATAAACCCAGGTGGGACGACAGTAGTGATGGCGCCGCCG
[-1]
3.4e-06
GGGGCGGCATGTGAA
+++ +++++++++ +
526 TATAATTCGACTTCCTTGTTGTTCATGCTTCCTTGATGACCAGGGTAGGTGTCAATGAGAGTGCATGTGGAAAGT
[+1]
2.0e-06
TTCACATGCCGCCCC
++++ ++++++ +++
601 TGCACCGGTTGTGAAATATGAGAAGCCTTTTCAATCTTCATATGCAAACCCACACATGCATCGTTGGTTTCTGTC
ACC1
sequence of the region upstream from YNR016C
LENGTH = 800 COMBINED P-VALUE = 8.22e-06 E-VALUE = 5.8e-05
DIAGRAM: 52-[-2]-9-[+1]-703
[-2]
2.5e-07
GCCGCCAGTGGCGATGTGGCC
+++ ++++ +++ ++ ++++
1 TATCCAAAGGGGAATGCTTCATCTTGTTGAACAACGCCCAACAATTTCCACTGCCCACCGAATCGTTGCGCCCGT
[+1]
8.8e-07
TTCACATGCCGCCCC
++++++++++++ +
76 TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAATTCAACCGCTCATTGCCA
CHO1
sequence of the region upstream from YER026C
LENGTH = 800 COMBINED P-VALUE = 3.22e-03 E-VALUE = 0.023
DIAGRAM: 162-[+1]-433-[+1]-14-[+1]-146
[+1]
6.4e-06
TTCACATGCCGCCCC
+++ +++ +++ +++
151 CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAGTATTAAGCATAATACAT
[+1] [+1]
4.5e-07 1.5e-06
TTCACATGCCGCCCC TTCACATGCCGCCCC
++++++ ++++++++ +++++++++++++ +
601 ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAAAGATGAAGATCCGTATT
CHO2
sequence of the region upstream from YGR157W
LENGTH = 800 COMBINED P-VALUE = 1.35e-02 E-VALUE = 0.094
DIAGRAM: 353-[+1]-109-[-1]-308
[+1]
1.2e-06
TTCACATGCCGCCCC
+++ +++++++++++
301 ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTCATGCCGCATTCATTATT
[-1]
1.2e-05
GGGGCGGCATGTGAA
+++ +++++ ++++
451 GTGGATCTCCGACACATGTGAATTTATAAGTAGGCATATGAAAATACAGATTCTTTCCACTGTGTTCCCTTTTAT
Debugging Information
CPU: chromo
Time 0.020000 secs.
mast meme.INO_up800.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