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 ./newsequences360.fasta (nucleotide)
	Last updated on Tue Aug 18 23:00:58 2015
	Database contains 101 sequences, 3535 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS ./meme.txt (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1     7   GGGTGTT

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

• Each of the following 21 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]
          5.3e-05
          GGGTGTT
          +++++++
1    ATTGTGGGTGTTTTGTCTGCCGCCTCTCTTGGTGT


437
  
  LENGTH = 35  COMBINED P-VALUE = 3.07e-03  E-VALUE =     0.31
  DIAGRAM: [-1]_28

     [-1]
     5.3e-05
     AACACCC
     +++++++
1    AACACCCTCTCCACCGGGCCCCGGGGGGCTCCCTT


435
  
  LENGTH = 35  COMBINED P-VALUE = 3.07e-03  E-VALUE =     0.31
  DIAGRAM: 21_[-1]_7

                          [-1]
                          5.3e-05
                          AACACCC
                          +++++++
1    TCCTCATCAACCGAGAGCCTGAACACCCTCCTCTC


459
  
  LENGTH = 35  COMBINED P-VALUE = 5.59e-03  E-VALUE =     0.56
  DIAGRAM: 14_[+1]_14

                   [+1]
                   9.7e-05
                   GGGTGTT
                   +++++++
1    TAGAAAGTGTGTTTGGGTGTGGATGCGGTATTCGC


436
  
  LENGTH = 35  COMBINED P-VALUE = 5.59e-03  E-VALUE =     0.56
  DIAGRAM: 28_[-1]

                                 [-1]
                                 9.7e-05
                                 AACACCC
                                 +++++++
1    CTTGAAACCGGCCACTGGGAGCCACCTCCACACCC


407
  
  LENGTH = 35  COMBINED P-VALUE = 5.59e-03  E-VALUE =     0.56
  DIAGRAM: 22_[+1]_6

                           [+1]
                           9.7e-05
                           GGGTGTT
                           +++++++
1    CTGGTCGTCCTACTACACAGCGGGGTGTGGAGGAG


376
  
  LENGTH = 35  COMBINED P-VALUE = 5.59e-03  E-VALUE =     0.56
  DIAGRAM: 21_[+1]_7

                          [+1]
                          9.7e-05
                          GGGTGTT
                          +++++++
1    TGGCCTCGCCTCCCTAGTTTGGGGTGTGGCGAGAG


451
  
  LENGTH = 35  COMBINED P-VALUE = 1.11e-02  E-VALUE =      1.1
  DIAGRAM: 35



424
  
  LENGTH = 35  COMBINED P-VALUE = 1.11e-02  E-VALUE =      1.1
  DIAGRAM: 35



401
  
  LENGTH = 35  COMBINED P-VALUE = 1.11e-02  E-VALUE =      1.1
  DIAGRAM: 35



439
  
  LENGTH = 35  COMBINED P-VALUE = 5.21e-02  E-VALUE =      5.3
  DIAGRAM: 35



430
  
  LENGTH = 35  COMBINED P-VALUE = 5.21e-02  E-VALUE =      5.3
  DIAGRAM: 35



420
  
  LENGTH = 35  COMBINED P-VALUE = 5.21e-02  E-VALUE =      5.3
  DIAGRAM: 35



450
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



449
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



440
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



419
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



413
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



389
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



385
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35



368
  
  LENGTH = 35  COMBINED P-VALUE = 6.74e-02  E-VALUE =      6.8
  DIAGRAM: 35

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

mast ./meme.txt -d ./newsequences360.fasta -ev 10.000000 -mt 0.000100