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MAST - Motif Alignment and Search Tool
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	MAST version 5.3.2 (Release date: Fri Feb 5 17:50:07 2021 -0800)

	For further information on how to interpret these results please access https://meme-suite.org/meme.
	To get a copy of the MAST software please access https://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 Sun Mar  1 14:58:12 2020
	Database contains 18 sequences, 1890 residues

	Scores for positive and reverse complement strands are combined.

	MOTIFS meme.crp0.de.oops.txt (nucleotide)
	MOTIF ID           ALT ID WIDTH BEST POSSIBLE MATCH
	----- ------------ ------ ----- -------------------
	    1 AHSGYAWWWAAT MEME-1    12 ACGGCAAATAAT
	    2 GTGADYDDDNTC MEME-2    12 GTGAGCGGTGTC

	PAIRWISE MOTIF CORRELATIONS:
	MOTIF     1
	----- -----
	   2   0.13
	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 18 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                           0.00023    105
bglr1                              76                              0.0098    105
tdc                                78                               0.043    105
deop2                              7 60                             0.055    105
pbr322                             53                               0.055    105
malk                               29 61                             0.14    105
tnaa                               71                                0.69    105
male                               14                                0.91    105
ara                                17 55                             0.94    105
cya                                50                                   1    105
ompa                               48                                 2.1    105
ilv                                39                                 2.6    105
gale                               42                                 3.1    105
malt                               41                                 3.2    105
crp                                63                                 4.5    105
ce1cg                              17 61                              4.8    105
trn9cat                            1 84                               5.9    105
uxu1                               17                                 6.6    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                                 0.00023  [+1]-2-[-2]-79
bglr1                                0.0098  79-[+2]-14
tdc                                   0.043  30-[+1]-39-[+2]-12
deop2                                 0.055  19-[+1]-74
pbr322                                0.055  58-[-2]-35
malk                                   0.14  32-[+2]-61
tnaa                                   0.69  105
male                                   0.91  105
ara                                    0.94  105
cya                                       1  105
ompa                                    2.1  105
ilv                                     2.6  105
gale                                    3.1  105
malt                                    3.2  105
crp                                     4.5  105
ce1cg                                   4.8  105
trn9cat                                 5.9  105
uxu1                                    6.6  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 = 1.30e-05  E-VALUE =  0.00023
  DIAGRAM: [+1]-2-[-2]-79

     [+1]          [-2]
     3.4e-06       7.2e-06
     ACGGCAAATAAT  GACACCGCTCAC
     ++++++++++++  ++  ++++++++
1    AACGCAATTAATGTGAGTTAGCTCACTCATTAGGCACCCCAGGCTTTACACTTTATGCTTCCGGCTCGTATGTTG


bglr1
  76
  LENGTH = 105  COMBINED P-VALUE = 5.42e-04  E-VALUE =   0.0098
  DIAGRAM: 79-[+2]-14

         [+2]
         9.1e-06
         GTGAGCGGTGTC
         ++++++  ++++
76   AACTGTGAGCATGGTCATATTTTTATCAAT


tdc
  78
  LENGTH = 105  COMBINED P-VALUE = 2.39e-03  E-VALUE =    0.043
  DIAGRAM: 30-[+1]-39-[+2]-12

                                   [+1]
                                   7.8e-05
                                   ACGGCAAATAAT
                                   ++++ +++++++
1    GATTTTTATACTTTAACTTGTTGATATTTAAAGGTATTTAATTGTAATAACGATACTCTGGAAAGTATTGAAAGT

           [+2]
           9.4e-05
           GTGAGCGGTGTC
           +++++++++  +
76   TAATTTGTGAGTGGTCGCACATATCCTGTT


deop2
  7 60
  LENGTH = 105  COMBINED P-VALUE = 3.05e-03  E-VALUE =    0.055
  DIAGRAM: 19-[+1]-74

                        [+1]
                        9.0e-05
                        ACGGCAAATAAT
                        ++++++++++++
1    AGTGAATTATTTGAACCAGATCGCATTACAGTGATGCAAACTTGTAAGTAGATTTCCTTAATTGTGATGTGTATC


pbr322
  53
  LENGTH = 105  COMBINED P-VALUE = 3.06e-03  E-VALUE =    0.055
  DIAGRAM: 58-[-2]-35

                                                               [-2]
                                                               9.4e-05
                                                               GACACCGCTCAC
                                                               ++ +++ +++++
1    CTGGCTTAACTATGCGGCATCAGAGCAGATTGTACTGAGAGTGCACCATATGCGGTGTGAAATACCGCACAGATG


malk
  29 61
  LENGTH = 105  COMBINED P-VALUE = 8.04e-03  E-VALUE =     0.14
  DIAGRAM: 32-[+2]-61

                                     [+2]
                                     7.1e-05
                                     GTGAGCGGTGTC
                                     ++++++++ + +
1    GGAGGAGGCGGGAGGATGAGAACACGGCTTCTGTGAACTAAACCGAGGTCATGTAAGGAATTTCGTGATGTTGCT


tnaa
  71 
  LENGTH = 105  COMBINED P-VALUE = 3.85e-02  E-VALUE =     0.69
  DIAGRAM: 105


male
  14
  LENGTH = 105  COMBINED P-VALUE = 5.05e-02  E-VALUE =     0.91
  DIAGRAM: 105


ara
  17 55
  LENGTH = 105  COMBINED P-VALUE = 5.22e-02  E-VALUE =     0.94
  DIAGRAM: 105


cya
  50
  LENGTH = 105  COMBINED P-VALUE = 5.58e-02  E-VALUE =        1
  DIAGRAM: 105


ompa
  48
  LENGTH = 105  COMBINED P-VALUE = 1.17e-01  E-VALUE =      2.1
  DIAGRAM: 105


ilv
  39
  LENGTH = 105  COMBINED P-VALUE = 1.46e-01  E-VALUE =      2.6
  DIAGRAM: 105


gale
  42
  LENGTH = 105  COMBINED P-VALUE = 1.70e-01  E-VALUE =      3.1
  DIAGRAM: 105


malt
  41
  LENGTH = 105  COMBINED P-VALUE = 1.78e-01  E-VALUE =      3.2
  DIAGRAM: 105


crp
  63
  LENGTH = 105  COMBINED P-VALUE = 2.48e-01  E-VALUE =      4.5
  DIAGRAM: 105


ce1cg
  17 61
  LENGTH = 105  COMBINED P-VALUE = 2.68e-01  E-VALUE =      4.8
  DIAGRAM: 105


trn9cat
  1 84
  LENGTH = 105  COMBINED P-VALUE = 3.26e-01  E-VALUE =      5.9
  DIAGRAM: 105


uxu1
  17
  LENGTH = 105  COMBINED P-VALUE = 3.66e-01  E-VALUE =      6.6
  DIAGRAM: 105

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CPU: Timothys-Mac-Mini.local
Time 0.006 secs.

mast -oc results/mast4 -nostatus /Users/t.bailey/meme_git/meme/tests/meme/meme.crp0.de.oops.txt common/crp0.s
