MAST version 3.0 (Release date: 2004/07/16 05:53:30)

For further information on how to interpret these results or to get a copy of the MAST software please access http://meme.sdsc.edu.

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 /home/meme/meme.3.0.6/tests/INO_up800.s (nucleotide)
	Last updated on Fri Jul 16 15:53:51 2004
	Database contains 7 sequences, 5600 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS meme.INO_up800.oops.4.Linuxx86_64.html (nucleotide)
	MOTIF WIDTH BEST POSSIBLE MATCH
	----- ----- -------------------
	  1    12   TTCACATGCCGC
	  2    10   TCTGGCACAG

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.32
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.281 C 0.222 G 0.229 T 0.267 

• Each of the following 7 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

  • 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]
            3.1e-07
            TTCACATGCCGC
            ++++++++++ +
76   TAAAATCTTCACATGGCCCGGCCGCGCGCGCGTTGTGCCAACAAGTCGCAGTCGAAATTCAACCGCTCATTGCCA

           [+2]
           7.4e-07
           TCTGGCACAG
           ++++++++++
226  TCGTATTCTGGCACAGTATAGCCTAGCACAATCACTGTCACAATTGTTATCGGTTCTACAATTGTTCTGCTCTCT

       [+2]
       3.9e-05
       TCTGGCACAG
       ++++++ +
151  CGTCTGGCGCCCTTCCCATTCCGAACCATGTTATATTGAACCATCTGGCGACAAGCAGTATTAAGCATAATACAT

                                      [-2]
                                      7.4e-07
                                      CTGTGCCAGA
                                      ++++++++++
526  CAATCCCCACTCCTTCTCAATGTGTGCAGACTTCTGTGCCAGACACTGAATATATATCAGTAATTGGTCAAAATC

               [+1]                         [+1]
               8.7e-07                      2.2e-05
               TTCACATGCCGC                 TTCACATGCCGC
               ++++++ +++ +                 +++++++++  +
601  ACTTTGAACGTTCACACGGCACCCTCACGCCTTTGAGCTTTCACATGGACCCATCTAAAGATGAAGATCCGTATT

                                                              [-2]
                                                              1.8e-05
                                                              CTGTGCCAGA
                                                              +++ +++ ++
226  ACGTTGTATATGAAACGAGTAGTGAACGTTCGTACGATCTTTCACGCAGACATGCGACTGCGCCCGCCGTAGACC

                        [-1]
                        4.2e-08
                        GCGGCATGTGAA
                        ++++++++++++
601  TGCGCTTCGGCGGCTAAATGCGGCATGTGAAAAGTATTGTCTATTTTATCTTCATCCTTCTTTCCCAGAATATTG

                [+1]
                1.3e-05
                TTCACATGCCGC
                +++++++++ ++
676  AACTTATTTAATTCACATGGAGCAGAGAAAGCGCACCTCTGCGTTGGCGGCAATGTTAATTTGAGACGTATATAA

                                                [+2]
                                                2.2e-05
                                                TCTGGCACAG
                                                ++ +++++ +
1    CCGGGTTATAGCAGCGTCTGCTCCGCATCACGATACACGAGGTGCAGGCACGGTTCACTACTCCCCTGGCCTCCA

                        [+1]
                        4.2e-08
                        TTCACATGCCGC
                        ++++++++++++
76   ACAAACGACGGCCAAAAACTTCACATGCCGCCCAGCCAAGCATAATTACGCAACAGCGATCTTTCCGTCGCACAA

                                        [-2]
                                        7.4e-07
                                        CTGTGCCAGA
                                        ++++++++++
151  GTTAATCTGATCAACGCTACGCCGATGACAACGGTCTGTGCCAGATCTGGTTTTCCCCACTTATTTGCTACTTCC

                                            [+1]
                                            5.8e-06
                                            TTCACATGCCGC
                                            ++++ ++ ++ +
301  AACTCCGTCAGGTCTTCCACGTGGAACTGCCAAGCCTCCTTCAGATCGCTCTTGTCGACCGTCTCCAAGAGATCC

                                                          [+1]
                                                          5.2e-07
                                                          TTCACATGCCGC
                                                          +++ ++++++++
301  ATATATATTTTTGCCTTGGTTTAAATTGGTCAAGACAGTCAATTGCCACACTTTTCTCATGCCGCATTCATTATT

                                          [-2]
                                          2.9e-05
                                          CTGTGCCAGA
                                          +  +++++++
376  CGCGAAGTTTTCCACACAAAACTGTGAAAATGAACGGCGATGCCAGAAACGGCAAAACCTCAAATGTTAGATAAC

                                       [-2]
                                       2.9e-05
                                       CTGTGCCAGA
                                         ++++++++
151  AACAGGGTGTCGGTCATACCGATAAAGCCGTCAAGAGTGCCAGAAAAGCAAGAAAGAACAAGATTAGATGTTGGT

                                              [+1]
                                              1.9e-06
                                              TTCACATGCCGC
                                              +++++++++  +
526  GCTTAGCAAAATCCAACCATTTTTTTTTTATCTCCCGCGTTTTCACATGCTACCTCATTCGCCTCGTAACGTTAC

CPU: chromo
Time 0.010000 secs.

mast meme.INO_up800.oops.4.Linuxx86_64.html -stdout