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 ./promotors_all.fasta (nucleotide)
	Last updated on Fri May 29 10:34:38 2015
	Database contains 2245 sequences, 76297 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS ./meme.html (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    10   TTTTTTTTCA

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

• Each of the following 124 sequences has E-value less than 50.
• 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]
       2.0e-06
       TGAAAAAAAA
       ++++++++++
1    CCTGAAAAAAAATTCATAAAAAGACTATCGTTTC

       [+1]
       2.0e-06
       TTTTTTTTCA
       ++++++++++
1    GGTTTTTTTTCATCACCAAAACGAATATCGGCAT

                            [+1]
                            2.0e-06
                            TTTTTTTTCA
                            ++++++++++
1    CGTCTTGTCAGTTTTTTGCCGCGTTTTTTTTCAG

                    [+1]
                    3.6e-06
                    TTTTTTTTCA
                    ++++++++++
1    CTGCCCTTGTTGCCGTTTTCTTTCAAACTCCTGA

                       [+1]
                       5.6e-06
                       TTTTTTTTCA
                       ++++++++++
1    AACGCCGACCACCCGGCCATTTTTTTCAACCAAA

       [+1]
       5.6e-06
       TTTTTTTTCA
       ++++++++++
1    TGATTTTTTTCAATTAACAACCAATTCTGCAAAG

          [+1]
          5.6e-06
          TTTTTTTTCA
          ++++++++++
1    TTCCGATTTTTTTCACGCTGCTCCCTCCTCGTTC

           [+1]
           7.2e-06
           TTTTTTTTCA
            +++++++++
1    TTTACCGTTTTTTTCACTCAATTTCATCAGTTTT

              [+1]
              8.8e-06
              TTTTTTTTCA
              ++++++++++
1    ATATTTGGGATTTCTTTCAGGGGCGGTCAGGTAG

     [+1]
     1.4e-05
     TTTTTTTTCA
     ++++++ +++
1    TTTTTTCTCATAACTATCAAAGCACGTCGTCAAT

                [+1]
                1.6e-05
                TTTTTTTTCA
                ++++++++ +
1    AGCACATGATATTTTTTTTGAACCCCAAACCATG

                 [-1]
                 1.6e-05
                 TGAAAAAAAA
                 + ++++++++
1    GGAAGAAAAACATCAAAAAAAAGGTTAAAGGATT

                [-1]
                1.6e-05
                TGAAAAAAAA
                + ++++++++
1    GGAGATCATCCTCAAAAAAAAAACATCGTGCTCC

                     [-1]
                     1.6e-05
                     TGAAAAAAAA
                     + ++++++++
1    GTTGCCCTGTAAATCATCAAAAAAAATAGAAGTT

                [-1]
                1.6e-05
                TGAAAAAAAA
                + ++++++++
1    TAATCAAAACTTCAAAAAAAATAACAGACTATCG

        [+1]
        2.4e-05
        TTTTTTTTCA
        +++++ ++++
1    TCGTTTTTCTTCATAACAAAATCATTCCAGAACC

                   [+1]
                   2.9e-05
                   TTTTTTTTCA
                   ++++++ +++
1    AAAACAACCGATACATTTTTCTCACCACACTGAC

          [+1]
          2.9e-05
          TTTTTTTTCA
          ++++++++ +
1    GGTGCTTTTCTTTGAACCAAAAGCACATTTGCCC

                            [+1]
                            3.6e-05
                            TTTTTTTTCA
                            +++++++++
1    ATGTCGGTCAAGGAAATGCATCCTTTTTTTTCTA

                       [+1]
                       3.6e-05
                       TTTTTTTTCA
                       +++++++++
1    CCTGACTGGACCTGCCTGTTTTTTTTCTTGCTGA

         [-1]
         3.6e-05
         TGAAAAAAAA
         + ++++++++
1    TCAATCAAAAAAATCAAAAAAGGAAGAATTCATT

               [+1]
               4.1e-05
               TTTTTTTTCA
                +++++++ +
1    AGAAAGTCGCGTTTTTTTGATCCGTTGCCTTTGT

       [+1]
       4.1e-05
       TTTTTTTTCA
       ++++++ +++
1    AAATTTTTATCAACCATAACCTTTCATCATTGCC

            [-1]
            4.1e-05
            TGAAAAAAAA
            + +++++++
1    CAGAATCTCAAAAAAACTTAAAGGTTAAGGAACA

       [+1]
       4.6e-05
       TTTTTTTTCA
       + ++++++++
1    AAAATTCTTTCACAACCATAACAGGTCCCTACGC

          [+1]
          5.0e-05
          TTTTTTTTCA
          +++++ ++++
1    CAGACATTTTCTTCAATACAAAACCGTATGACCA

      [+1]
      5.0e-05
      TTTTTTTTCA
      +++++ ++++
1    GATTTTCTTCAACCTCTCAAGAAAGAACCGACGA

                          [+1]
                          5.0e-05
                          TTTTTTTTCA
                            ++++++++
1    TCCGCCATTTCCAAGCACTTCGATTCTTTCAACC

                   [+1]
                   6.1e-05
                   TTTTTTTTCA
                   +++++++++
1    CTCCGGATTCCTGCTTTTCTTTCTGACTCGCTCC

          [+1]
          6.1e-05
          TTTTTTTTCA
          ++++ +++++
1    AACACTTTTATTTCAAGAAGGTTCGCCTATTGAT

           [+1]
           6.1e-05
           TTTTTTTTCA
           ++++ +++++
1    GAGTTTTTTTATTTCATTATTTTGACAGATCGAT

          [-1]
          6.9e-05
          TGAAAAAAAA
           +++++++++
1    CGCCGAGAAAAAAATAACCAAACTATAGAAAGCA

                            [-1]
                            6.9e-05
                            TGAAAAAAAA
                             +++++++++
1    CTATACCCCTTCAATCCAAACGGAGAAAAAAATC

                  [-1]
                  7.9e-05
                  TGAAAAAAAA
                  + + ++++++
1    GGATTTTGCATCTTCAGAAAAAAGCGGCCTGAAG

     [+1]
     7.9e-05
     TTTTTTTTCA
     +++++++++
1    TTTTTTTTCGATCAAGAGCAAGCGAAGCAACAAA

                        [+1]
                        7.9e-05
                        TTTTTTTTCA
                        +++++++++
1    ACCTCGACATTCACCACATATTTTTTTCCCATCT

          [+1]
          8.2e-05
          TTTTTTTTCA
           ++++++++
1    GAGAGGTTTTTTTCCTAACCATGTCTGAAGGCTG

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

mast ./meme.html -d ./promotors_all.fasta -ev 50.000000 -mt 0.000100