EXIT
MAST - Motif Alignment and Search Tool
MAST version 4.1.1 (Release date: Tue Apr 21 15:00:06 PDT 2009)
For further information on how to interpret these results or to get
a copy of the MAST software please access http://meme.nbcr.net.
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 ./seed.fasta (peptide)
Last updated on Thu May 20 20:03:54 2010
Database contains 8 sequences, 2005 residues
MOTIFS ./memeout.txt (peptide)
MOTIF WIDTH BEST POSSIBLE MATCH
----- ----- -------------------
1 50 PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
2 50 MYFGCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
3 32 KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD
PAIRWISE MOTIF CORRELATIONS:
MOTIF 1 2
----- ----- -----
2 0.13
3 0.19 0.19
No overly similar pairs (correlation > 0.60) found.
Random model letter frequencies (from non-redundant database):
A 0.073 C 0.018 D 0.052 E 0.062 F 0.040 G 0.069 H 0.022 I 0.056 K 0.058
L 0.092 M 0.023 N 0.046 P 0.051 Q 0.041 R 0.052 S 0.074 T 0.059 V 0.064
W 0.013 Y 0.033
SECTION I: HIGH-SCORING SEQUENCES
- Each of the following 8 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
|
|---|
|
| >THIM_BACSU/10-258
|
| 2.9e-82
| 249
|
|
| >THIM_ECOLI/15-259
|
| 1.8e-58
| 245
|
|
| >THIM_SALTY/15-259
|
| 7.8e-56
| 245
|
|
| >THIM_HAEIN/8-255
|
| 1.3e-54
| 248
|
|
| >THIM_ARCFU/14-256
|
| 2.3e-41
| 243
|
|
| >THI4_SCHPO/246-500
|
| 4.1e-41
| 255
|
|
| >THIM_HELPY/2-249
|
| 6.8e-39
| 248
|
|
| >THI6_YEAST/255-526
|
| 3.8e-16
| 272
|
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
- Spacers and motif occurences are indicated by
- Spacers and motif occurences are indicated by
- occurrence of motif `n' with p-value less than 0.0001.
- Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.
| Links | Name | Expect | Motifs
|
|---|
|
| >THIM_BACSU/10-258
| 2.9e-82
|
|
|
| >THIM_ECOLI/15-259
| 1.8e-58
|
|
|
| >THIM_SALTY/15-259
| 7.8e-56
|
|
|
| >THIM_HAEIN/8-255
| 1.3e-54
|
|
|
| >THIM_ARCFU/14-256
| 2.3e-41
|
|
|
| >THI4_SCHPO/246-500
| 4.1e-41
|
|
|
| >THIM_HELPY/2-249
| 6.8e-39
|
|
|
| >THI6_YEAST/255-526
| 3.8e-16
|
|
| SCALE
|
| | |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| |
| 1 |
25 |
50 |
75 |
100 |
125 |
150 |
175 |
200 |
225 |
250 |
|
|---|
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,
- the position p-value of the occurrence,
- the best possible match to the motif, and
- columns whose match to the motif has a positive score (indicated
by a plus sign).
THIM_BACSU/10-258
LENGTH = 249 COMBINED P-VALUE = 3.62e-83 E-VALUE = 2.9e-82
DIAGRAM: 8-[1]-42-[3]-17-[2]-50
[1]
2.3e-47
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
++++++++++++++++++++++++++++++++++++++++++++++++++
1 LTAVRRHSPLVHSITNNVVTNFTANGLLALGASPVMAYAKEEVADMAKIAGALVLNIGTLSKESVEAMIIAGKSA
[3] [
7.6e-06 1
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD M
+ +++ ++++++ ++ ++ + +
76 NEHGVPVILDPVGAGATPFRTESARDIIREVRLAAIRGNAAEIAHTVGVTDWLIKGVDAGEGGGDIIRLAQQAAQ
2]
.2e-42
YFGCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
+++++++++++++++++++++++++++++++++++++++++++++++++
151 KLNTVIAITGEVDVIADTSHVYTLHNGHKLLTKVTGAGCLLTSVVGAFCAVEENPLFAAIAAISSYGVAAQLAAQ
THIM_ECOLI/15-259
LENGTH = 245 COMBINED P-VALUE = 2.30e-59 E-VALUE = 1.8e-58
DIAGRAM: 8-[1]-41-[3]-16-[2]-48
[1]
1.6e-27
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
+++++ ++ ++ ++++ ++++++++++++ ++++ +++++++++++ +
1 LHLFHQHSPLVHCMTNDVVQTFTANTLLALGASPAMVIETEEASQFAAIASALLINVGTLTQPRAQAMRAAVEQA
[3] [2]
2.1e-18 7.9
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD MYF
+++ +++ +++++++++ +++++ ++++++ +++
76 KSSQTPWTLDPVAVGALDYRRHFCHELLSFKPAAIRGNASEIMALAGIANGGRGVDTTDAAANAIPAAQTLARET
e-26
GCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
++ + ++++ ++++++ + + +++++++++++ ++++++ +++++ +
151 GAIVVVTGEMDYVTDGHRIIGIHGGDPLMTKVVGTGCALSAVVAACCALPGDTLENVASACHWMKQAGERAVARS
THIM_SALTY/15-259
LENGTH = 245 COMBINED P-VALUE = 9.79e-57 E-VALUE = 7.8e-56
DIAGRAM: 8-[1]-41-[3]-16-[2]-48
[1]
1.1e-27
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
+++++ ++ ++ ++++ ++++++++++++++ ++ +++++++++++ +
1 LKHFRALSPLTHCMTNDVVQTFTANTLLALGASPAMVIDPVEARPFAAIANALLINVGTLTASRADAMRAAVESA
[3] [2]
4.2e-17 2.7
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD MYF
+++ +++ ++++++++++++ + ++++++ +
76 YDAKTPWTLDPVAVGALEFRRRFCLDLLSLRPAAIRGNASEILALSGMALGGRGVDTTEAALAALPAAQALARQI
e-24
GCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
+ + +++++++++++ +++++ +++++++++ ++++++ +++++ +
151 DCIVVVTGEIDYVTNGQRTLSIPGGDPLMTRIVGTGCALSAVVAASCALPGAALDNVASACCWMKLAGQAAAERS
THIM_HAEIN/8-255
LENGTH = 248 COMBINED P-VALUE = 1.63e-55 E-VALUE = 1.3e-54
DIAGRAM: 8-[1]-42-[3]-16-[2]-50
[1]
1.8e-29
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
++++ +++++++++++++++++++++ + + ++ ++ +++++++++++
1 LSKIREQNPLIHNITNIVAANFSANGLLALGASPLMSANVEEMQEVPKISQALVINIGTLIGKDREAMLQAGKTA
[3] [2
1.3e-14 8.
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD MY
+++ +++ ++++++++ ++++ + +++++ ++
76 NEVGIPVVLDPVGVGATSYRRETIRELLAEVKFALIRGNAGELAAIAGETWQAKGVDAGQGEVDLKAVAEKVAQR
]
8e-24
FGCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
++ ++++++++++++++++++++++ + +++ ++++ ++ ++++
151 YGCTVLISGAVDIVSDGTQTATVHNGTSLFPKVTASGCLLSAVCAAFLAVSEGNYFSATLEACVAYTIAGECAAQ
THIM_ARCFU/14-256
LENGTH = 243 COMBINED P-VALUE = 2.88e-42 E-VALUE = 2.3e-41
DIAGRAM: 8-[1]-41-[3]-14-[2]-48
[1]
5.8e-22
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
+ ++ ++++++++++++ ++++++++ + + + +++++++++++
1 IARIAEFKPVVHHITNYVAMNDSANITIAIGASPIMSFAHGEIDELVSIASSLLINIGTLDEYIIQAVMLAVKSA
[3] [2]
1.5e-09 7.3e-
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD MYFGC
+ + +++++ ++++++ + +++++ ++++
76 KSKGVPVLLDPVGSGATKLRTSTALSVAEEGVDVIKGNQGEILSLLRKEGVVRGVDSKVTAEAADVKEVARKFGL
23
VFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
++ +++ +++++++ +++ +++ +++ +++ +++++++++++
151 VVVATGKEDLISDGRSVYVMRNGTEMLGRITASGCMLGSVIASFMAVQKDFLLASLEGLACYNVAGELAAEKSSG
THI4_SCHPO/246-500
LENGTH = 255 COMBINED P-VALUE = 5.13e-42 E-VALUE = 4.1e-41
DIAGRAM: 8-[1]-40-[3]-18-[2]-57
[1]
5.9e-26
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
++++ +++ ++ ++++++ +++ ++ +++ +++++++++ ++++++++
1 LQKLKDFTPLIHHLTNAVAKNFSANVTLAAYGSPTMGESYDEVADFAKAPGALVLNIGILENTKTYIHAAQVNND
[3] [2
1.0e-08 1.
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD MY
++ ++++ +++ +++ ++ ++++ +
76 LARPVILDPVAVGATTARSKVINTLLNYAYYDIIKGNEGEIMNLAGEQGLMRGVDSISQHTLAARITAVHRLAVE
]
6e-19
FGCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
++++ +++++++++++ ++++ ++ +++ +++ +++++++ ++
151 RRCVVAMSGAVDVISDGNSTYVIKNGNPLLGQITASGCSLGSVMGVTASICQNDKLLAAITATLLYNIASELAVE
THIM_HELPY/2-249
LENGTH = 248 COMBINED P-VALUE = 8.54e-40 E-VALUE = 6.8e-39
DIAGRAM: 8-[1]-42-[3]-15-[2]-51
[1]
7.0e-28
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
++++ +++++++ +++++++++++++ + ++ ++ + +++++++ ++++
1 LKELRQKRPLVHNITNYVAAQFVANGLLALGASPLMSDAIDEMRDLAKISDALAINIGTLNDRAILCAKEAIKHY
[3] [2]
3.2e-09 8.9
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD MYF
+++ ++++++ ++ +++++ ++ + ++
76 KALNKPIVLDPVGCSASALRHDTSLELLKSGGISALRGNAAELGSLVGISCESKGLDSNDAATPVEIIKLAAQKY
e-15
GCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
++ ++++++++ ++++ ++ + + +++++++ + ++++
151 SVIAVMTGKTDYVSDGKKVLSITGGSEYLALITGAGCLHAAACASFLSLKKDPLDSMAQLCALYKQAAFNAQKKV
THI6_YEAST/255-526
LENGTH = 272 COMBINED P-VALUE = 4.72e-17 E-VALUE = 3.8e-16
DIAGRAM: 8-[1]-41-[3]-40-[2]-51
[1]
8.0e-16
PLIHCITNCVSCNWCANMLLALGCKPVMAYHKEWVPDFTKQSQALWINIG
+++ +++ + ++ +++ +++++++++ + ++++ + + ++ ++
1 ISQVSNNRPLVQHITNKVHQNFGANVTLALGSSPIMSEIESEVSELARIPNASLLLNTGSVAPIEMLKAAINAYN
[3]
4.0e-06
KFLLNCHPTVIRGNMSEIKALYGRKHHGKGVD
++ ++++ +++++++ + +
76 EVNRPITFDPVGYSATETRLCLNNTLLTYGQFACIKGNCSEILSLAKLNNHKMKGVDSSSGKTNIDTLVRATQIV
[2]
1.2e-06
MYFGCVFAVTGPTDYVTDGNHTYTIHNGHPMMTWVTGTGCMLTGLIASFC
+ + + +++ + +++ ++ ++++++ +++++
151 AFQYRTVAVCTGEFDCVADGTFGGEYKLSSGTEGITAEDLPCVIIEDGPIPIMGDITASGCSLGSTIASFIGGLD
Debugging Information
CPU: kodomo-count
Time 0.052003 secs.
mast ./memeout.txt -d ./seed.fasta -ev 10.000000 -mt 0.000100
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