MAST version 4.3.0 (Release date: Sat Sep 26 01:51:56 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.

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 ./seed.fasta (peptide)
	Last updated on Tue May 24 13:57:05 2011
	Database contains 59 sequences, 18553 residues

	MOTIFS ./memeout.txt (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    50   GKRVVMVDDSIVRGTTSRRIVKMLRDAGATEVHMRISSPPVMHPCFYGID
	  2    50   GVPDSSIPAAIGYAEQSGIPYFMGLIKNRYVHRTFIQPTQHLREQGVRMK
	  3    40   CVFEYIYFARPDSNMDGQNVHSVRKRMGKMLAQESPVPAD

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1     2
	----- ----- -----
	   2   0.09
	   3   0.14  0.12
	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 

• Each of the following 15 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.

• 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

  • n

    occurrence of motif `n' with p-value less than 0.0001.

  • 1

    Sequences longer than 1000 are not shown to scale and are indicated by thicker lines.

• 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).

                                                [2]
                                                4.0e-07
                                                GVPDSSIPAAIGYAEQSGIPYFMGLIKNRYVH
                                                +    +++       ++ + + +    +  ++
1    CGVGFVAELSGETTRKTVTDSLEMLIRMTHRGACGCESNTGDGAGILVGLPHDFYAEAATELGFVLPSAGNYAVG

     
     
     RTFIQPTQHLREQGVRMK
       +   + + ++ +  +
76   MFFLPTVESRREESKNVFTKVAESLGHSVLGWRLVPTDNSGLGNSALQTEPIIAQVFLTPTTKSKADFEQQMYIL

                                                       [3]
                                                       4.1e-05
                                                       CVFEYIYFARPDSNMDGQNVHSVRK
                                                        +   +  +          ++ +++
76   VFLPQDSAIAAETKQVAEKIIAEEGLTLLGWRSVPVQPEVLGVQARDNQPLIEQLIVQSEVADEELERKLYVARK

     
     
     RMGKMLAQESPVPAD
     ++  +++    +  +
151  RIHRTLAVRPEAGFDELYVCSFSTRTIVYKGMVRSEILGKFYLDLQNPEYKTTFALYHRRFSTNTMPKWQLAQPM

                                 [1]
                                 4.7e-05
                                 GKRVVMVDDSIVRGTTSRRIVKMLRDAGATEVHMRISSPPVMHPCFY
                                       + +     +  +++ +    + + + +   +   +++
1    CGIVGAIAQRDVAEILLEGLRRLEYRGYDSAGLAVVDAEGHMTRLRRLGKVQMLAQAAEEHPLHGGTGIAHTRWA

     
     
     GID
     
76   THGEPSEVNAHPHVSEHIVVVHNGIIENHEPLREELKARGYTFVSETDTEVIAHLVNWELKQGGTLREAVLRAIP

                                        [3]
                                        7.1e-05
                                        CVFEYIYFARPDSNMDGQNVHSVRKRMGKMLAQESPVPAD
                                        +    +     ++++  + + ++     +   +    +++
1    CGIFGYCNYLVERSRGEIIDTLVDGLQRLEYRGYDSTGIAIDGDEADSTFIYKQIGKVSALKEEITKQNPNRDVT

                        [3]
                        5.4e-06
                        CVFEYIYFARPDSNMDGQNVHSVRKRMGKMLAQESPVPAD
                        + ++        +  +++ + +   + + + ++    + +
301  WTENTHMSKEKRAFYEYHSSLMEPWDGPTAISFTDGKQIGAILDRNGLRPARYYVTKDDYIIFSSEV

                        [3]
                        1.9e-05
                        CVFEYIYFARPDSNMDGQNVHSVRKRMGKMLAQESPVPAD
                        ++++        +  ++  + ++  + + +  +    +
301  WQNDKTMPQEKRDFYQWAACVMEPWDGPALISFTDGRYIGAVLDRNGLRPSRFYVTKENVLVMASEV

                                                [2]
                                                6.1e-05
                                                GVPDSSIPAAIGYAEQSGIPYFMGLIKNRYVH
                                                +     ++    + +      +   ++   ++
1    CGVGLVVSISGTPSRKVVESGIAALKAVWHRGAVDADGKTGDGAGIHVQIPVKFFYDQIRRTGHEPTCTKLVAVG

     
     
     RTFIQPTQHLREQGVRMK
       +   ++   +   +
76   QVFLPRTDLSGQERCRTIVESEVLRMGHYIYGWRHVPVDTSVLGEKANATRPEIEQILIRCEKDIDDEQFERELY

                                                   [1]
                                                   5.2e-05
                                                   GKRVVMVDDSIVRGTTSRRIVKMLRDAGA
                                                     + + + +   ++    +   +++
76   LPVDGTEDAVSRIETIAHEEGLTVLGWREVPVAPQMLGATARSTMPVFRQVFVGDGASRGIALDRHAFALRKRAE

     
     
     TEVHMRISSPPVMHPCFYGID
      +  +   +       + +
151  REAGVYFPSLSARTIVYKGMLTTGQLEPFFPDLSDRRFASAIALVHSRFSTNTFPSWPLAHPYRFVAHNGEINTV

CPU: kodomo
Time 0.024001 secs.

mast ./memeout.txt -d ./seed.fasta -ev 10.000000 -mt 0.000100