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.

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 Fri May 21 01:46:27 2010
	Database contains 5 sequences, 782 residues

	MOTIFS ./memeout.txt (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    41   DSFQVDHTKMKAPYVRVAKVMQTPKGDKISNFDLRFCQPNK
	  2    29   IDCSPMGCRTGFYMSLWGTPSSQDVAKAW
	  3    36   WGDVPGTNIYQCGNYRMHSLFMAKYWARKWLAQGIS

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1     2
	----- ----- -----
	   2   0.10
	   3   0.09  0.09
	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 5 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).

        [1]
        4.7e-38
        DSFQVDHTKMKAPYVRVAKVMQTPKGDKISNFDLRFCQPNK
        +++++++++++++++++++++++++++++++++++++++++
1    PSVESFELDHNAVVAPYVRHCGVHKVGTDGVVNKFDIRFCQPNKQAMKPDTIHTLEHLLAFTIRSHAEKYDHFDI

     [2]                                   [3]
     2.7e-26                               9.7e-26
     IDCSPMGCRTGFYMSLWGTPSSQDVAKAW         WGDVPGTNIYQCGNYRMHSLFMAKYWARKWLAQGIS
     +++++++++++++++++++++++++++++         +++++++++++++++++++++++++ ++++++++++
76   IDISPMGCQTGYYLVVSGEPTSAEIVDLLEDTMKEAVEITEIPAANEKQCGQAKLHDLEGAKRLMRFWLSQDKEE

        [1]                                                                    [
        2.6e-38                                                                6
        DSFQVDHTKMKAPYVRVAKVMQTPKGDKISNFDLRFCQPNK                              I
        +++++++++++++++++++++ +++++ +++++++++++++                              +
1    PLLDSFTVDHTRMEAPAVRVAKTMNTPHGDAITVFDLRFCVPNKEVMPERGIHTLEHLFAGFMRNHLNGNGVEII

     2]                                      [3]
     .6e-28                                  2.3e-15
     DCSPMGCRTGFYMSLWGTPSSQDVAKAW            WGDVPGTNIYQCGNYRMHSLFMAKYWARKWLAQGI
     ++++++++++++++++++++++ +++++            ++ +++++ ++++++ ++++ +++++++ ++  +
76   DISPMGCRTGFYMSLIGTPDEQRVADAWKAAMEDVLKVQDQNQIPELNVYQCGTYQMHSLQEAQDIARSILERDV

     
     
     S
     
151  RINSNEELALP

        [1]                                                                    [
        2.2e-36                                                                1
        DSFQVDHTKMKAPYVRVAKVMQTPKGDKISNFDLRFCQPNK                              I
        ++++++++++++++++ ++++ +++++ +++++++++++++                              +
1    PLLDSFKVDHTKMNAPAVRIAKTMLTPKGDNITVFDLRFCIPNKEILSPKGIHTLEHLFAGFMRDHLNGDSIEII

     2]                                      [3]
     .3e-21                                  8.0e-19
     DCSPMGCRTGFYMSLWGTPSSQDVAKAW            WGDVPGTNIYQCGNYRMHSLFMAKYWARKWLAQGI
     +++++++++++++++++++ ++ +  ++            ++ ++++++++++ ++ ++++ + ++++++++ ++
76   DISPMGCRTGFYMSLIGTPNEQKVSEAWLASMQDVLGVQDQASIPELNIYQCGSYTEHSLEDAHEIAKNVIARGI

     
     
     S
     +
151  GVNKNEDLSLD

        [1]                                                                [2]
        5.3e-22                                                            3.5e-
        DSFQVDHTKMKAPYVRVAKVMQTPKGDKISNFDLRFCQPNK                          IDCSP
        +++ ++++++++++++ ++  ++  ++ + +++ ++ +++                           +++++
1    MNVESFNLDHTKVKAPYVRIADRKKGVNGDLIVKYDVRFKQPNRDHMDMPSLHSLEHLVAEIIRNHANYVVDWSP

                                      [3]
     12                               3.0e-12
     MGCRTGFYMSLWGTPSSQDVAKAW         WGDVPGTNIYQCGNYRMHSLFMAKYWARKWLAQGIS
     +++++++++ +      +++   +           ++++ ++++++ ++ + +++++  ++ ++++  +
76   MGCQTGFYLTVLNHDNYTEILEVLEKTMQDVLKAKEVPASNEKQCGWAANHTLEGAQNLARAFLDKRAEWSEVG

                                                                             [2]
                                                                             5.6
                                                                             IDC
                                                                             +++
1    KKITSFTIDHTKLNPGIYVSRKDTFENVIFTTIDIRIKAPNIEPIIENAAIHTIEHIGATLLRNNEVWTEKIVYF

                                         [3]
     e-18                                6.5e-14
     SPMGCRTGFYMSLWGTPSSQDVAKAW          WGDVPGTNIYQCGNYRMHSLFMAKYWARKWLAQGIS
     ++++++++++++  +++ +++ +++            + +++++ +++++++ +++++++++  +++    +
76   GPMGCRTGFYLIIFGDYESKDLVDLVSWLFSEIVNFSEPIPGASDKECGNYKEHNLDMAKYESSKYLQILNNIKE

CPU: kodomo-count
Time 0.028002 secs.

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