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 ./all.fasta (nucleotide)
	Last updated on Fri May 29 15:07:27 2015
	Database contains 1631 sequences, 29358 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS ./meme.txt (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    18   GCTCAACAAGAAGGCCAA

	Random model letter frequencies (from non-redundant database):
	A 0.274 C 0.225 G 0.225 T 0.274 

• Each of the following 49 sequences has E-value less than 30.
• 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

  • sn

    occurrence of motif `n' with p-value less than 0.0001. A minus sign indicates that the occurrence is on the reverse complement strand.

  • 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 (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).

     [+1]
     2.7e-07
     GCTCAACAAGAAGGCCAA
     + ++++++ +++++ +++
1    GATCAACATGAAGGGCAT

     [+1]
     1.1e-06
     GCTCAACAAGAAGGCCAA
     ++++ + +++++++++++
1    GGTCCCGAAGGAGGACAT

     [+1]
     3.8e-06
     GCTCAACAAGAAGGCCAA
     +++ +++++++++ ++++
1    CGTGAACACGAACCAGAA

     [+1]
     4.2e-06
     GCTCAACAAGAAGGCCAA
     +  +++++++++++++++
1    GTACGAAAAGGACGCCGA

     [+1]
     6.5e-06
     GCTCAACAAGAAGGCCAA
     +++ ++++ +++++ +++
1    GCTTGCAAGGAAGGGGAA

     [+1]
     7.1e-06
     GCTCAACAAGAAGGCCAA
     +++++ +++  +++++++
1    GCTCATCACTTACGCCGA

     [+1]
     1.1e-05
     GCTCAACAAGAAGGCCAA
     ++++++  ++++++ +++
1    CCTCAATTCGAAGGTGGT

     [+1]
     3.1e-05
     GCTCAACAAGAAGGCCAA
     +++ ++ ++ +++++++
1    CGTGGCGAAAGAGGCCGG

CPU: kodomo.fbb.msu.ru
Time 0.004000 secs.

mast ./meme.txt -d ./all.fasta -ev 30.000000 -mt 0.000100