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MEME - Motif discovery tool
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MEME version 5.5.3 (Release date: Sat Jun 10 16:19:38 2023 -0700)

For further information on how to interpret these results please access https://meme-suite.org/meme.
To get a copy of the MEME Suite 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 Charles Elkan,
"Fitting a mixture model by expectation maximization to
discover motifs in biopolymers",
Proceedings of the Second International Conference on Intelligent Systems
for Molecular Biology, pp. 28-36, AAAI Press, Menlo Park, California, 1994.
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TRAINING SET
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PRIMARY SEQUENCES= common/crp0.s
CONTROL SEQUENCES= Primary sequences shuffled preserving 2-mers
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
ce1cg                    1.0000    105  ara                      1.0000    105  
bglr1                    1.0000    105  crp                      1.0000    105  
cya                      1.0000    105  deop2                    1.0000    105  
gale                     1.0000    105  ilv                      1.0000    105  
lac                      1.0000    105  male                     1.0000    105  
malk                     1.0000    105  malt                     1.0000    105  
ompa                     1.0000    105  tnaa                     1.0000    105  
uxu1                     1.0000    105  pbr322                   1.0000    105  
trn9cat                  1.0000    105  tdc                      1.0000    105  
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COMMAND LINE SUMMARY
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This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme -p 4 common/crp0.s -oc results/meme28 -mod oops -dna -revcomp -nmotifs 2 -objfun se -w 12 -hsfrac 0.6 -shuf 2 -nostatus 

model:  mod=          oops    nmotifs=         2    evt=           inf
objective function:           em=       Selective mHG
                              starts=   log likelihood ratio (LLR)
strands: + -
width:  minw=           12    maxw=           12
nsites: minsites=       18    maxsites=       18    wnsites=       0.8
theta:  spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            1890    N=              18
sample: seed=            0    hsfrac=        0.6
        searchsize=   1890    norand=         no    csites=         -1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304 
Background letter frequencies (from file dataset with add-one prior applied):
A 0.304 C 0.196 G 0.196 T 0.304 
Background model order: 0
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MOTIF AHSGYAWWWAAT MEME-1	width =  12  sites =  18  llr = 103  p-value = 9.5e-002  E-value = 9.5e-002
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	Motif AHSGYAWWWAAT MEME-1 Description
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Simplified        A  931127654551
pos.-specific     C  :34253::122:
probability       G  ::571:11:123
matrix            T  14::3:446217

         bits    2.4             
                 2.1             
                 1.9             
                 1.6             
Relative         1.4 *           
Entropy          1.2 * **        
(8.3 bits)       0.9 * ** *      
                 0.7 * ** *     *
                 0.5 * *******  *
                 0.2 ************
                 0.0 ------------

Multilevel           ATGGCAAATAAT
consensus             ACCTCTTACCG
sequence              C        G 
                                 
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	Motif AHSGYAWWWAAT MEME-1 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
lac                          +      1  4.67e-06          . AACGCAATTAAT GTGAGTTAGC
tdc                          +     31  9.21e-05 TTGATATTTA AAGGTATTTAAT TGTAATAACG
deop2                        +     20  1.06e-04 TTTGAACCAG ATCGCATTACAG TGATGCAAAC
pbr322                       -     45  1.23e-04 GGTATTTCAC ACCGCATATGGT GCACTCTCAG
male                         +      6  1.86e-04      ACATT ACCGCCAATTCT GTAACAGAGA
bglr1                        +      5  1.86e-04       ACAA ATCCCAATAACT TAATTATTGG
cya                          +     36  2.38e-04 ATCTTTCTTT ACGGTCAATCAG CAAGGTGTTA
ara                          +     33  3.35e-04 GTCTATAATC ACGGCAGAAAAG TCCACATTGA
malk                         +     55  5.01e-04 GAGGTCATGT AAGGAATTTCGT GATGTTGCTT
tnaa                         +     45  7.27e-04 ATCTTTAAAA AAAGCATTTAAT ATTGCTCCCC
crp                          +     16  7.95e-04 AGCGAAAGCT ATGCTAAAACAG TCAGGATGCT
gale                         -     89  9.43e-04      GGCTT ATGGTATGAAAT AACCATAGCA
trn9cat                      -     73  1.73e-03 ACGTCTCATT TTCGCCAAAAGT TGGCCCAGGG
uxu1                         +     32  1.99e-03 TGATGTGGTT AACCCAATTAGA ATTCGGGATT
ilv                          -     74  2.93e-03 AGGGGAGACA ATGGAAAATTTT TCAGCAAAGG
malt                         +     76  3.73e-03 CACATAAAAA AACGTCATCGCT TGCATTAGAA
ompa                         -     36  3.95e-03 CGTCAGGCAT ATGAAAAAAAAG TCTTGTATAA
ce1cg                        -     34  4.66e-03 CTTTCACACC ACGCGCTATTCT CGCCCGATGC
--------------------------------------------------------------------------------

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	Motif AHSGYAWWWAAT MEME-1 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
lac                               4.7e-06  [+1]_93
tdc                               9.2e-05  30_[+1]_63
deop2                             0.00011  19_[+1]_74
pbr322                            0.00012  44_[-1]_49
male                              0.00019  5_[+1]_88
bglr1                             0.00019  4_[+1]_89
cya                               0.00024  35_[+1]_58
ara                               0.00033  32_[+1]_61
malk                               0.0005  54_[+1]_39
tnaa                              0.00073  44_[+1]_49
crp                                0.0008  15_[+1]_78
gale                              0.00094  88_[-1]_5
trn9cat                            0.0017  72_[-1]_21
uxu1                                0.002  31_[+1]_62
ilv                                0.0029  73_[-1]_20
malt                               0.0037  75_[+1]_18
ompa                               0.0039  35_[-1]_58
ce1cg                              0.0047  33_[-1]_60
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	Motif AHSGYAWWWAAT MEME-1 in BLOCKS format
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BL   MOTIF AHSGYAWWWAAT width=12 seqs=18
lac                      (    1) AACGCAATTAAT  1 
tdc                      (   31) AAGGTATTTAAT  1 
deop2                    (   20) ATCGCATTACAG  1 
pbr322                   (   45) ACCGCATATGGT  1 
male                     (    6) ACCGCCAATTCT  1 
bglr1                    (    5) ATCCCAATAACT  1 
cya                      (   36) ACGGTCAATCAG  1 
ara                      (   33) ACGGCAGAAAAG  1 
malk                     (   55) AAGGAATTTCGT  1 
tnaa                     (   45) AAAGCATTTAAT  1 
crp                      (   16) ATGCTAAAACAG  1 
gale                     (   89) ATGGTATGAAAT  1 
trn9cat                  (   73) TTCGCCAAAAGT  1 
uxu1                     (   32) AACCCAATTAGA  1 
ilv                      (   74) ATGGAAAATTTT  1 
malt                     (   76) AACGTCATCGCT  1 
ompa                     (   36) ATGAAAAAAAAG  1 
ce1cg                    (   34) ACGCGCTATTCT  1 
//

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	Motif AHSGYAWWWAAT MEME-1 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 6.53916 E= 9.5e-002 
   163  -1081  -1081   -245 
    13     50  -1081     35 
  -245    118    135  -1081 
  -245     18    188  -1081 
   -87    135   -182    -13 
   125     50  -1081  -1081 
    87  -1081   -182     35 
    72  -1081   -182     55 
    35   -182  -1081     87 
    72     18    -82    -87 
    72     18     18   -245 
  -245  -1081     50    113 
--------------------------------------------------------------------------------

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	Motif AHSGYAWWWAAT MEME-1 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 9.5e-002 
 0.944444  0.000000  0.000000  0.055556 
 0.333333  0.277778  0.000000  0.388889 
 0.055556  0.444444  0.500000  0.000000 
 0.055556  0.222222  0.722222  0.000000 
 0.166667  0.500000  0.055556  0.277778 
 0.722222  0.277778  0.000000  0.000000 
 0.555556  0.000000  0.055556  0.388889 
 0.500000  0.000000  0.055556  0.444444 
 0.388889  0.055556  0.000000  0.555556 
 0.500000  0.222222  0.111111  0.166667 
 0.500000  0.222222  0.222222  0.055556 
 0.055556  0.000000  0.277778  0.666667 
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	Motif AHSGYAWWWAAT MEME-1 regular expression
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A[TAC][GC][GC][CT][AC][AT][AT][TA][AC][ACG][TG]
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Time  0.36 secs.

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MOTIF GTGADYDDDNTC MEME-2	width =  12  sites =  18  llr = 109  p-value = 9.7e-001  E-value = 9.7e-001
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	Motif GTGADYDDDNTC MEME-2 Description
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Simplified        A  :117413433:1
pos.-specific     C  1::314111229
probability       G  819:3233222:
matrix            T  18::23434371

         bits    2.4             
                 2.1   *         
                 1.9   *         
                 1.6   *        *
Relative         1.4 * *        *
Entropy          1.2 * *        *
(8.7 bits)       0.9 ****       *
                 0.7 ****      **
                 0.5 **** *    **
                 0.2 ********  **
                 0.0 ------------

Multilevel           GTGAACTATATC
consensus               CGTAGAT  
sequence                 T GTGG  
                                 
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	Motif GTGADYDDDNTC MEME-2 sites sorted by position p-value
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Sequence name            Strand  Start   P-value                Site  
-------------            ------  ----- ---------            ------------
bglr1                        +     80  7.14e-06 GTTAATAACT GTGAGCATGGTC ATATTTTTAT
lac                          +     13  2.30e-05 CGCAATTAAT GTGAGTTAGCTC ACTCATTAGG
malk                         +     33  5.66e-05 CACGGCTTCT GTGAACTAAACC GAGGTCATGT
tdc                          +     82  7.48e-05 AAGTTAATTT GTGAGTGGTCGC ACATATCCTG
pbr322                       -     59  7.48e-05 TTACGCATCT GTGCGGTATTTC ACACCGCATA
deop2                        +     64  8.59e-05 TTCCTTAATT GTGATGTGTATC GAAGTGTGTT
ompa                         -     54  2.22e-04 ACTTACAAGT GTGAACTCCGTC AGGCATATGA
tnaa                         -     77  2.44e-04 TTGTTTAAAT GTGAATCGAATC ACAATCGTTC
ilv                          +     43  3.72e-04 AGTACAAAAC GTGATCAACCCC TCAATTTTCC
malt                         -     47  4.06e-04 GTGTCTGAAT TTGCACTGTGTC ACAATTCCAA
ce1cg                        +     65  6.24e-04 GACTGTTTTT TTGATCGTTTTC ACAAAAATGG
ara                          -     53  1.04e-03 GTGTGACGCC GTGCAAATAATC AATGTGGACT
cya                          -     56  1.32e-03 GGTCTAAAAC GTGATCAATTTA ACACCTTGCT
gale                         +     28  1.43e-03 AAATTCTTGT GTAAACGATTCC ACTAATTTAT
male                         +     46  1.54e-03 AGCGACGGTG GGGCGTAGGGGC AAGGAGGATG
trn9cat                      +     88  2.19e-03 TGGCGAAAAT GAGACGTTGATC GGCACG    
crp                          +     57  3.58e-03 CATTGATGTA CTGCATGTATGC AAAGGACGTC
uxu1                         +      6  4.01e-03      CCCAT GAGAGTGAAATT GTTGTGATGT
--------------------------------------------------------------------------------

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	Motif GTGADYDDDNTC MEME-2 block diagrams
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SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
bglr1                             7.1e-06  79_[+2]_14
lac                               2.3e-05  12_[+2]_81
malk                              5.7e-05  32_[+2]_61
tdc                               7.5e-05  81_[+2]_12
pbr322                            7.5e-05  58_[-2]_35
deop2                             8.6e-05  63_[+2]_30
ompa                              0.00022  53_[-2]_40
tnaa                              0.00024  76_[-2]_17
ilv                               0.00037  42_[+2]_51
malt                              0.00041  46_[-2]_47
ce1cg                             0.00062  64_[+2]_29
ara                                 0.001  52_[-2]_41
cya                                0.0013  55_[-2]_38
gale                               0.0014  27_[+2]_66
male                               0.0015  45_[+2]_48
trn9cat                            0.0022  87_[+2]_6
crp                                0.0036  56_[+2]_37
uxu1                                0.004  5_[+2]_88
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	Motif GTGADYDDDNTC MEME-2 in BLOCKS format
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BL   MOTIF GTGADYDDDNTC width=12 seqs=18
bglr1                    (   80) GTGAGCATGGTC  1 
lac                      (   13) GTGAGTTAGCTC  1 
malk                     (   33) GTGAACTAAACC  1 
tdc                      (   82) GTGAGTGGTCGC  1 
pbr322                   (   59) GTGCGGTATTTC  1 
deop2                    (   64) GTGATGTGTATC  1 
ompa                     (   54) GTGAACTCCGTC  1 
tnaa                     (   77) GTGAATCGAATC  1 
ilv                      (   43) GTGATCAACCCC  1 
malt                     (   47) TTGCACTGTGTC  1 
ce1cg                    (   65) TTGATCGTTTTC  1 
ara                      (   53) GTGCAAATAATC  1 
cya                      (   56) GTGATCAATTTA  1 
gale                     (   28) GTAAACGATTCC  1 
male                     (   46) GGGCGTAGGGGC  1 
trn9cat                  (   88) GAGACGTTGATC  1 
crp                      (   57) CTGCATGTATGC  1 
uxu1                     (    6) GAGAGTGAAATT  1 
//

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	Motif GTGADYDDDNTC MEME-2 position-specific scoring matrix
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log-odds matrix: alength= 4 w= 12 n= 1692 bayes= 6.53916 E= 9.7e-001 
 -1081   -182    209   -145 
  -145  -1081   -182    145 
  -245  -1081    227  -1081 
   125     50  -1081  -1081 
    35   -182     77    -45 
  -245    118    -23     13 
   -13   -182     50     35 
    35   -182     50    -13 
   -13    -82     18     35 
    13    -23     18    -13 
 -1081    -23    -23    113 
  -245    218  -1081   -245 
--------------------------------------------------------------------------------

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	Motif GTGADYDDDNTC MEME-2 position-specific probability matrix
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letter-probability matrix: alength= 4 w= 12 nsites= 18 E= 9.7e-001 
 0.000000  0.055556  0.833333  0.111111 
 0.111111  0.000000  0.055556  0.833333 
 0.055556  0.000000  0.944444  0.000000 
 0.722222  0.277778  0.000000  0.000000 
 0.388889  0.055556  0.333333  0.222222 
 0.055556  0.444444  0.166667  0.333333 
 0.277778  0.055556  0.277778  0.388889 
 0.388889  0.055556  0.277778  0.277778 
 0.277778  0.111111  0.222222  0.388889 
 0.333333  0.166667  0.222222  0.277778 
 0.000000  0.166667  0.166667  0.666667 
 0.055556  0.888889  0.000000  0.055556 
--------------------------------------------------------------------------------

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	Motif GTGADYDDDNTC MEME-2 regular expression
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GTG[AC][AGT][CT][TAG][AGT][TAG][ATG]TC
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Time  0.65 secs.

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SUMMARY OF MOTIFS
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	Combined block diagrams: non-overlapping sites with p-value < 0.0001
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SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ce1cg                            2.42e-01  105
ara                              4.94e-02  105
bglr1                            5.06e-04  79_[+2(7.14e-06)]_14
crp                              2.51e-01  105
cya                              5.44e-02  105
deop2                            2.87e-03  63_[+2(8.59e-05)]_30
gale                             1.63e-01  105
ilv                              1.31e-01  105
lac                              1.36e-05  [+1(4.67e-06)]_2_[-2(5.54e-06)]_79
male                             4.97e-02  105
malk                             7.58e-03  32_[+2(5.66e-05)]_61
malt                             1.59e-01  105
ompa                             1.04e-01  105
tnaa                             3.53e-02  105
uxu1                             3.56e-01  105
pbr322                           2.89e-03  58_[-2(7.48e-05)]_35
trn9cat                          3.17e-01  105
tdc                              2.24e-03  30_[+1(9.21e-05)]_39_[+2(7.48e-05)]_\
    12
--------------------------------------------------------------------------------

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Stopped because requested number of motifs (2) found.
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CPU: Timothys-iMac.local

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