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MAST - Motif Alignment and Search Tool
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	MAST version 5.0.0 (Release date: Wed Oct 11 17:39:42 2017 -0700)

	For further information on how to interpret these results or to get
	a copy of the MAST software please access http://meme-suite.org .
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REFERENCE
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	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.
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DATABASE AND MOTIFS
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	DATABASE crp0.s (nucleotide)
	Last updated on Tue Feb  2 11:33:11 2016
	Database contains 18 sequences, 1890 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS meme.crp0.cd.zoops.txt (nucleotide)
	MOTIF ID            ALT ID WIDTH BEST POSSIBLE MATCH
	----- ------------- ------ ----- -------------------
	    1 RWAWRYKGWGKGR MEME-1    13 GAAAGCGGAGGGG
	    2 ATTCCTDA      MEME-2     8 ATTCCTAA

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.26
	No overly similar pairs (correlation > 0.60) found.

	Random model letter frequencies (from non-redundant database):
	A 0.274 C 0.225 G 0.225 T 0.274 
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SECTION I: HIGH-SCORING SEQUENCES
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	- Each of the following 12 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
	    o finding the score of the single best match of each motif
	      to the sequence (best matches may overlap),
	    o calculating the sequence p-value of each score,
	    o forming the product of the p-values,
	    o 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.
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SEQUENCE NAME                      DESCRIPTION                   E-VALUE  LENGTH
-------------                      -----------                   -------- ------
lac                                9 80                             0.042    105
pbr322                             53                               0.052    105
ilv                                39                               0.075    105
malk                               29 61                             0.23    105
bglr1                              76                                0.59    105
uxu1                               17                                 1.2    105
ompa                               48                                 1.7    105
deop2                              7 60                               2.2    105
male                               14                                 2.6    105
ara                                17 55                                5    105
malt                               41                                 7.6    105
cya                                50                                 9.1    105

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SECTION II: MOTIF DIAGRAMS
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	- 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
	   o -d-    `d' residues separate the end of the preceding motif 
		    occurrence and the start of the following motif occurrence
	   o [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.
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SEQUENCE NAME                      E-VALUE   MOTIF DIAGRAM
-------------                      --------  -------------
lac                                   0.042  67-[+1]-25
pbr322                                0.052  47-[+1]-45
ilv                                   0.075  50-[-1]-42
malk                                   0.23  53-[-2]-44
bglr1                                  0.59  50-[+2]-47
uxu1                                    1.2  105
ompa                                    1.7  105
deop2                                   2.2  105
male                                    2.6  105
ara                                       5  105
malt                                    7.6  105
cya                                     9.1  105

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SECTION III: ANNOTATED SEQUENCES
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	- 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
	   o the motif number of the occurrence (a minus sign indicates that
	  the occurrence is on the reverse complement strand),
	   o the position p-value of the occurrence,
	   o the best possible match to the motif (or its reverse complement), and
	   o columns whose match to the motif has a positive score (indicated 
	     by a plus sign).
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lac
  9 80
  LENGTH = 105  COMBINED P-VALUE = 2.33e-03  E-VALUE =    0.042
  DIAGRAM: 67-[+1]-25

                                                                        [+1]
                                                                        4.5e-06
                                                                        GAAAGCGG
                                                                        ++++++++
1    AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG

     
     
     AGGGG
     +++++
76   TGTGGAATTGTGAGCGGATAACAATTTCAC


pbr322
  53
  LENGTH = 105  COMBINED P-VALUE = 2.91e-03  E-VALUE =    0.052
  DIAGRAM: 47-[+1]-45

                                                    [+1]
                                                    4.5e-06
                                                    GAAAGCGGAGGGG
                                                    +++++++++++++
1    CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG


ilv
  39
  LENGTH = 105  COMBINED P-VALUE = 4.18e-03  E-VALUE =    0.075
  DIAGRAM: 50-[-1]-42

                                                       [-1]
                                                       4.5e-06
                                                       CCCCTCCGCTTTC
                                                       +++++++++++++
1    GCTCCGGCGGGGTTTTTTGTTATCTGCAATTCAGTACAAAACGTGATCAACCCCTCAATTTTCCCTTTGCTGAAA


malk
  29 61
  LENGTH = 105  COMBINED P-VALUE = 1.26e-02  E-VALUE =     0.23
  DIAGRAM: 53-[-2]-44

                                                          [-2]
                                                          4.3e-05
                                                          TTAGGAAT
                                                          ++++++++
1    GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT


bglr1
  76
  LENGTH = 105  COMBINED P-VALUE = 3.27e-02  E-VALUE =     0.59
  DIAGRAM: 50-[+2]-47

                                                       [+2]
                                                       4.3e-05
                                                       ATTCCTAA
                                                       ++++++++
1    ACAAATCCCAATAACTTAATTATTGGGATTTGTTATATATAACTTTATAAATTCCTAAAATTACACAAAGTTAAT


uxu1
  17
  LENGTH = 105  COMBINED P-VALUE = 6.55e-02  E-VALUE =      1.2
  DIAGRAM: 105


ompa
  48
  LENGTH = 105  COMBINED P-VALUE = 9.55e-02  E-VALUE =      1.7
  DIAGRAM: 105


deop2
  7 60
  LENGTH = 105  COMBINED P-VALUE = 1.21e-01  E-VALUE =      2.2
  DIAGRAM: 105


male
  14
  LENGTH = 105  COMBINED P-VALUE = 1.46e-01  E-VALUE =      2.6
  DIAGRAM: 105


ara
  17 55
  LENGTH = 105  COMBINED P-VALUE = 2.78e-01  E-VALUE =        5
  DIAGRAM: 105


malt
  41
  LENGTH = 105  COMBINED P-VALUE = 4.21e-01  E-VALUE =      7.6
  DIAGRAM: 105


cya
  50
  LENGTH = 105  COMBINED P-VALUE = 5.06e-01  E-VALUE =      9.1
  DIAGRAM: 105

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CPU: Timothys-iMac.rd.unr.edu
Time 0.004 secs.

mast -oc results/mast7 -nostatus meme/meme.crp0.cd.zoops.txt common/crp0.s
