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 ./meme.fasta (nucleotide)
	Last updated on Fri May  1 16:46:19 2015
	Database contains 99 sequences, 3465 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS ./meme.txt (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    11   CAGGGGGTTTA

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

• Each of the following 30 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

  • 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]
      4.8e-06
      CAGGGGGTTTA
      +++++++++++
1    ACTAGGGTTTTATTTTTCATGTGATTGGAACCATT


78NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.39e-04  E-VALUE =    0.024
  DIAGRAM: 1_[+1]_23

      [+1]
      4.8e-06
      CAGGGGGTTTA
      +++++++++++
1    ACTAGGGTTTTATTTTTCATGTGATTGGAACCATT


43NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 3.71e-04  E-VALUE =    0.037
  DIAGRAM: 19_[+1]_5

                        [+1]
                        7.4e-06
                        CAGGGGGTTTA
                        +++++++++++
1    AAATGAAAGGGTATCAACAATAGGGGTTTAAAATT


8NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 4.37e-04  E-VALUE =    0.043
  DIAGRAM: 23_[+1]_1

                            [+1]
                            8.7e-06
                            CAGGGGGTTTA
                            +++++++++++
1    AATAAAACCGATATTATAACTAAAAGGGGGTTTTA


13NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.16e-03  E-VALUE =     0.11
  DIAGRAM: 23_[+1]_1

                            [+1]
                            2.3e-05
                            CAGGGGGTTTA
                            +++++++++ +
1    TTAGCATCAATTTTTGTTTGGATAAAGGGGTTCAA


70NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.14e-03  E-VALUE =     0.21
  DIAGRAM: 12_[+1]_12

                 [+1]
                 4.3e-05
                 CAGGGGGTTTA
                 +++++++++ +
1    CAAAAAATATTAAAAGGGTTTAAAAGTTTTTGTTT


6NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.14e-03  E-VALUE =     0.21
  DIAGRAM: 20_[+1]_4

                         [+1]
                         4.3e-05
                         CAGGGGGTTTA
                         +++++++++++
1    GCCATCAAATTTACCGATAGCTAGGCTTTTAATCT


55NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.43e-03  E-VALUE =     0.24
  DIAGRAM: 21_[+1]_3

                          [+1]
                          4.9e-05
                          CAGGGGGTTTA
                          +++++++++ +
1    CCCGATCAACAATCAAAAATAAAAGGGGTTATTGA


67NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 3.45e-03  E-VALUE =     0.34
  DIAGRAM: 1_[+1]_23

      [+1]
      6.9e-05
      CAGGGGGTTTA
      +++++++++++
1    TCTAGGCTTTTTGGGTTTAAAAGCACAGTCAGGCT


29NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 3.80e-03  E-VALUE =     0.38
  DIAGRAM: [+1]_24

     [+1]
     7.6e-05
     CAGGGGGTTTA
     ++++++ ++ +
1    CTAGGGATTAAAGGGTGTCCTAAAATAAGCATGTT


36NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 4.68e-03  E-VALUE =     0.46
  DIAGRAM: 17_[+1]_7

                      [+1]
                      9.4e-05
                      CAGGGGGTTTA
                      ++++++ +++
1    ACTTTTAACAAACAATTCAAGGGATTTGGCGATTT


33NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 4.68e-03  E-VALUE =     0.46
  DIAGRAM: 18_[+1]_6

                       [+1]
                       9.4e-05
                       CAGGGGGTTTA
                       +++++++++++
1    CTTTCTTAATTCCTGTAAATGCGGTTTTAAATCTT


30NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 4.68e-03  E-VALUE =     0.46
  DIAGRAM: 18_[+1]_6

                       [+1]
                       9.4e-05
                       CAGGGGGTTTA
                       ++++++ ++ +
1    ACCCACACAATAATGAGTAAGGGGATTAAAATTCT


40NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 5.16e-03  E-VALUE =     0.51
  DIAGRAM: 35



4NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 6.96e-03  E-VALUE =     0.69
  DIAGRAM: 35



71NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.01e-02  E-VALUE =        1
  DIAGRAM: 35



68NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.01e-02  E-VALUE =        1
  DIAGRAM: 35



11NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.01e-02  E-VALUE =        1
  DIAGRAM: 35



50NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.29e-02  E-VALUE =      1.3
  DIAGRAM: 35



26NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.29e-02  E-VALUE =      1.3
  DIAGRAM: 35



53NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 1.74e-02  E-VALUE =      1.7
  DIAGRAM: 35



42NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.00e-02  E-VALUE =        2
  DIAGRAM: 35



76NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.14e-02  E-VALUE =      2.1
  DIAGRAM: 35



44NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.14e-02  E-VALUE =      2.1
  DIAGRAM: 35



7NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 2.62e-02  E-VALUE =      2.6
  DIAGRAM: 35



89NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 3.37e-02  E-VALUE =      3.3
  DIAGRAM: 35



5NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 3.77e-02  E-VALUE =      3.7
  DIAGRAM: 35



64NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 4.43e-02  E-VALUE =      4.4
  DIAGRAM: 35



19NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 5.97e-02  E-VALUE =      5.9
  DIAGRAM: 35



83NC_000921.1
  NC_000921.1 Helicobacter pylori J99 chromosome, complete genome
  LENGTH = 35  COMBINED P-VALUE = 9.43e-02  E-VALUE =      9.3
  DIAGRAM: 35

CPU: kodomo.fbb.msu.ru
Time 0.000000 secs.

mast ./meme.txt -ev 10.000000 -mt 0.000100