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 Sun May 26 14:16:39 2013
	Database contains 4 sequences, 782 residues

	MOTIFS ./meme.txt (peptide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    31   IVAVRQGNILATSFHPELTDDTRWHQYFVEM
	  2    29   NPYQPHLGGMDITVCRNYYGRQVDSFETD
	  3    21   IESGKPVWGTCAGMIWLAKKV

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1     2
	----- ----- -----
	   2   0.11
	   3   0.20  0.11
	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 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 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).

                                                                    [3]
                                                                    9.7e-18
                                                                    IESGKPVWGTCA
                                                                    ++++++++++++
1    VLGLQGAVREHIHAIEACGAAGLVVKRPEQLNEVDGLILPGGESTTMRRLIDTYQFMEPLREFAAQGKPMFGTCA

               [2]
               1.0e-22
     GMIWLAKKV NPYQPHLGGMDITVCRNYYGRQVDSFETD
     +++ +++++   ++++++++++ ++++++++++++++++
76   GLIILAKEIAGSDNPHLGLLNVVVERNSFGRQVDSFEADLTIKGLDEPFTGVFIRAPHILEAGENVEVLSEHNGR

     [1]
     2.2e-26
     IVAVRQGNILATSFHPELTDDTRWHQYFVEM
     +++++++ ++++++++++++++++ ++++++
151  IVAAKQGQFLGCSFHPELTEDHRVTQLFVEMVEE

                                                                 [3]
                                                                 5.7e-10
                                                                 IESGKPVWGTCAGMI
                                                                   + ++++++++++
1    VLAIQGDVEEHEEAIKKAGYEAKKVKRVEDLEGIDALIIPGGESTAIGKLMKKYGLLEKIKNSNLPILGTCAGMV

           [2]                                                              [1]
           5.7e-16                                                          2.0e
     WLAKKVNPYQPHLGGMDITVCRNYYGRQVDSFETD                                    IVAV
     ++++     + ++ +++++++++++++++++++ +                                    ++++
76   LLSKGTGINQILLELMDITVKRNAYGRQVDSFEKEIEFKDLGKVYGVFIRAPVVDKILSDDVEVIARDGDKIVGV

     
     -11
     RQGNILATSFHPELTDDTRWHQYFVEM
     ++++ ++ +++++++++ +    ++ +
151  KQGKYMALSFHPELSEDGYKVYKYFVENCVK

                                                                               [
                                                                               1
                                                                               I
                                                                               +
1    VLALQGAFIEHVRHVEKCIVENRDFYEKKLSVMTVKDKNQLAQCDALIIPGGESTAMSLIAERTGFYDDLYAFVH

     3]                     [2]
     .1e-09                 2.2e-11
     ESGKPVWGTCAGMIWLAKKV   NPYQPHLGGMDITVCRNYYGRQVDSFETD
       ++ +++++++++  +++     +   ++ ++ +++++++++++ ++
76   NPSKVTWGTCAGLIYISQQLSNEAKLVKTLNLLKVKVKRNAFGRQAQSSTRICDFSNFIPHCNDFPATFIRAPVI

                               [1]
                               8.0e-11
                               IVAVRQGNILATSFHPELTDDTRWHQYFVEM
                                 + ++++++++++++++ + +   + ++
151  EEVLDPEHVQVLYKLDGKDNGGQELIVAAKQKNNILATSFHPELAENDIRFHDWFIREFVL

                                                                             [3]
                                                                             3.9
                                                                             IES
                                                                             +
1    VLALQGAFLEHTNHLKRCLAENDYGIKIEIKTVKTPEDLAQCDALIIPGGESTSMSLIAQRTGLYPCLYEFVHNP

                          [2]
     e-11                 8.3e-11
     GKPVWGTCAGMIWLAKKV   NPYQPHLGGMDITVCRNYYGRQVDSFETD
      + ++++++++++++ +         +++++ + +++++++++ +++
76   EKVVWGTCAGLIFLSAQLENESALVKTLGVLKVDVRRNAFGRQAQSFTQKCDFSNFIPGCDNFPATFIRAPVIER

                          [1]
                          8.8e-09
                          IVAVRQGNILATSFHPELTDDTRWHQYFVEM
                            + +  +++++++++++ + +   + ++
151  ILDPIAVKSLYELPVNGKDVVVAATQNHNILVTSFHPELADSDTRFHDWFIRQFVS

CPU: kodomo.fbb.msu.ru
Time 0.008000 secs.

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