Command line Training Set First Motif Summary of Motifs Termination Explanation


Search sequence databases with these motifs using MAST.
Submit these motifs to BLOCKS multiple alignment processor.
Build and use a motif-based hidden Markov model (HMM) using Meta-MEME.


MEME - Motif discovery tool

MEME version 3.5.1 (Release date: 2006/02/01 02:08:55)

For further information on how to interpret these results or to get a copy of the MEME software please access http://meme.nbcr.net.

This file may be used as input to the MAST algorithm for searching sequence databases for matches to groups of motifs. MAST is available for interactive use and downloading at http://meme.nbcr.net.


REFERENCE

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.


TRAINING SET

DATAFILE= A0037.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
X00371                   1.0000    501  extracted09              1.0000    500  
galGal2_xenoRefGene_NM_2 1.0000    500  danRer3_refGene_NM_20058 1.0000    500  

COMMAND LINE SUMMARY

This information can also be useful in the event you wish to report a
problem with the MEME software.

command: meme /home/meme/meme351/LOGS/meme.27006.data -dna -mod zoops -nmotifs 20 -maxsites 4 -minw 6 -maxw 15 -evt 1e100 -revcomp -time 7200 -maxsize 60000 -nostatus -maxiter 20 

model:  mod=         zoops    nmotifs=        20    evt=        1e+100
object function=  E-value of product of p-values
width:  minw=            6    maxw=           15    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=        4    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        20
        distance=    1e-05
data:   n=            2001    N=               4
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.235 C 0.265 G 0.265 T 0.235 
Background letter frequencies (from dataset with add-one prior applied):
A 0.235 C 0.265 G 0.265 T 0.235 

P N
MOTIF 1     width = 15     sites = 4     llr = 67     E-value = 5.3e+002

SimplifiedA:a:aa:3:3a:::33
pos.-specificCa:a:::3:8:a5::8
probabilityG::::::58:::::8:
matrixT:::::a:3:::5a::
bits 2.1      
1.9         
1.7         
1.5         
Information 1.3         
content 1.0              
(24.3 bits)0.8              
0.6              
0.4               
0.2               
0.0
Multilevel CACAATGGCACCTGC
consensus ATATAA
sequence C
NAME STRAND START P-VALUE    SITES 
extracted09+2759.63e-10 TCCTAGCTCCCACAATGGCACTTGCCCCAAAATAG
X00371+3182.05e-09 CCTGCCTCGCCACAATGGCACCTGCCCTAAAATAG
galGal2_xenoRefGene_NM_2+2762.31e-08 CAGTGGCACTCACAATAGCACCTGACCCGAAATAG
danRer3_refGene_NM_20058-476.57e-08 TCAAAACACACACAATCTAACTTACACTCACTGAC

Motif 1 block diagrams

NameLowest
p-value
   Motifs
extracted09 9.6e-10

+1
X00371 2e-09

+1
galGal2_xenoRefGene_NM_2 2.3e-08

+1
danRer3_refGene_NM_20058 6.6e-08

-1
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 1 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 1 position-specific scoring matrix


Motif 1 position-specific probability matrix


to known motifs in JASPAR database.





Time  0.38 secs.


P N
MOTIF 2     width = 15     sites = 4     llr = 67     E-value = 8.3e+002

SimplifiedA:::33:::::::3::
pos.-specificC::a88:::8:::5::
probabilityG3a::::::3:a:35a
matrixT8::::aaa:a:a:5:
bits 2.1     
1.9         
1.7         
1.5         
Information 1.3          
content 1.0              
(24.2 bits)0.8              
0.6              
0.4               
0.2               
0.0
Multilevel TGCCCTTTCTGTCGG
consensus GAAGAT
sequence G
NAME STRAND START P-VALUE    SITES 
galGal2_xenoRefGene_NM_2+2049.63e-10 GTTTGGGCAATGCCCTTTCTGTCTGGCGTGGGACA
X00371+2122.05e-09 GCTTCTGTGGTGCCCTTTCTGTCGGCTATGAGAGT
extracted09+1865.91e-09 GTGGCTTCGGTGCCCTTTCTGTGGGCTTGTGCAAG
danRer3_refGene_NM_20058+908.69e-08 GAGTGTATGTGGCAATTTGTGTATGAATGAGTGTG

Motif 2 block diagrams

NameLowest
p-value
   Motifs
galGal2_xenoRefGene_NM_2 9.6e-10

+2
X00371 2e-09

+2
extracted09 5.9e-09

+2
danRer3_refGene_NM_20058 8.7e-08

+2
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 2 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 2 position-specific scoring matrix


Motif 2 position-specific probability matrix


to known motifs in JASPAR database.





Time  0.71 secs.


P N
MOTIF 3     width = 15     sites = 4     llr = 64     E-value = 2.7e+003

SimplifiedA:::a:a8a3a3585a
pos.-specificCa3::::3:8:3::5:
probabilityG::::8::::::5:::
matrixT:8a:3:::::5:3::
bits 2.1      
1.9       
1.7       
1.5       
Information 1.3          
content 1.0              
(23.0 bits)0.8              
0.6               
0.4               
0.2               
0.0
Multilevel CTTAGAAACATAAAA
consensus CTCAAGTC
sequence C
NAME STRAND START P-VALUE    SITES 
extracted09+1102.40e-09 TGTGCCCAAGCTTAGAAACATGACAAGTCCCTGTG
X00371+1312.40e-09 GGTGGCCAAGCTTAGAAACATGACAGGTCCTCTTG
galGal2_xenoRefGene_NM_2+3047.55e-08 GAAATAGCTTCCTAGAAAAAAAAAAGAGAGGCTGA
danRer3_refGene_NM_20058-171.58e-07 CTGACACACACTTATACACACATAAGCACACACAT

Motif 3 block diagrams

NameLowest
p-value
   Motifs
extracted09 2.4e-09

+3
X00371 2.4e-09

+3
galGal2_xenoRefGene_NM_2 7.5e-08

+3
danRer3_refGene_NM_20058 1.6e-07

-3
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 3 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 3 position-specific scoring matrix


Motif 3 position-specific probability matrix


to known motifs in JASPAR database.





Time  1.03 secs.


P N
MOTIF 4     width = 15     sites = 4     llr = 62     E-value = 4.6e+003

SimplifiedA:8a8::3a3a38::a
pos.-specificC::::::5::::::::
probabilityGa:::a83:8:8:33:
matrixT:3:3:3:::::388:
bits 2.1    
1.9      
1.7      
1.5      
Information 1.3           
content 1.0              
(22.4 bits)0.8              
0.6              
0.4               
0.2               
0.0
Multilevel GAAAGGCAGAGATTA
consensus TTTAAATGG
sequence G
NAME STRAND START P-VALUE    SITES 
extracted09+3207.59e-10 GAGGGCCAGAGAAAGGCAGAGATTAGACCCCTGGA
X00371+3639.99e-09 GAGGGCTAGAGAAAGGAAAAGATTAGACCCTCCCT
galGal2_xenoRefGene_NM_2+2453.42e-08 AGTCCAATACGAAAGGCAGAAATGATGCCATCAGT
danRer3_refGene_NM_20058+724.50e-07 TGTGTTTTGAGTATGTGAGAGTGTATGTGGCAATT

Motif 4 block diagrams

NameLowest
p-value
   Motifs
extracted09 7.6e-10

+4
X00371 1e-08

+4
galGal2_xenoRefGene_NM_2 3.4e-08

+4
danRer3_refGene_NM_20058 4.5e-07

+4
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 4 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 4 position-specific scoring matrix


Motif 4 position-specific probability matrix


to known motifs in JASPAR database.





Time  1.34 secs.


P N
MOTIF 5     width = 7     sites = 4     llr = 38     E-value = 5.0e+003

SimplifiedA:a:a8aa
pos.-specificC:::::::
probabilityG:::::::
matrixTa:a:3::
bits 2.1      
1.9      
1.7      
1.5      
Information 1.3       
content 1.0       
(13.8 bits)0.8       
0.6       
0.4       
0.2       
0.0
Multilevel TATAAAA
consensus T
sequence
NAME STRAND START P-VALUE    SITES 
galGal2_xenoRefGene_NM_2+4023.98e-05 GAGGAGGGGCTATAAAACCCGCGGGTG
extracted09+4143.98e-05 TCTGGGAAGGTATAAAAGCCCTTCAGG
X00371+4693.98e-05 TCCCAGAAGGTATAAAAACGCCCTTGG
danRer3_refGene_NM_20058+4537.95e-05 AGAGATGTTGTATATAAAGTCAATGTG

Motif 5 block diagrams

NameLowest
p-value
   Motifs
galGal2_xenoRefGene_NM_2 4e-05

+5
extracted09 4e-05

+5
X00371 4e-05

+5
danRer3_refGene_NM_20058 8e-05

+5
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 5 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 5 position-specific scoring matrix


Motif 5 position-specific probability matrix


to known motifs in JASPAR database.





Time  1.63 secs.


P N
MOTIF 6     width = 15     sites = 4     llr = 62     E-value = 8.7e+003

SimplifiedA::3:::3:::3:5:a
pos.-specificC:a:8:a:a3a::38:
probabilityG::::3:::::5::::
matrixTa:838:8:8:3a33:
bits 2.1   
1.9       
1.7       
1.5       
Information 1.3           
content 1.0             
(22.3 bits)0.8             
0.6              
0.4               
0.2               
0.0
Multilevel TCTCTCTCTCGTACA
consensus ATGACACT
sequence TT
NAME STRAND START P-VALUE    SITES 
extracted09+18.55e-10 TCTCTCTCTCGTACATGTACATGCA
X00371-3871.26e-08 TCCTTCACTTTCTCTCTCTCATCCAGGGAGGGTCT
danRer3_refGene_NM_20058-1551.20e-07 ACACACACACTCACTCACTCGTATACACACTGATA
galGal2_xenoRefGene_NM_2-3443.11e-07 CAGCTGGACATCTTGCTCCCTTTCAGGCTTGACTA

Motif 6 block diagrams

NameLowest
p-value
   Motifs
extracted09 8.5e-10
+6
X00371 1.3e-08

-6
danRer3_refGene_NM_20058 1.2e-07

-6
galGal2_xenoRefGene_NM_2 3.1e-07

-6
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 6 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 6 position-specific scoring matrix


Motif 6 position-specific probability matrix


to known motifs in JASPAR database.





Time  1.94 secs.


P N
MOTIF 7     width = 15     sites = 2     llr = 41     E-value = 2.6e+004

SimplifiedAaaaa:a:::::::a:
pos.-specificC:::::::a::aaa::
probabilityG::::::a::5:::::
matrixT::::a:::a5::::a
bits 2.1         
1.9              
1.7              
1.5              
Information 1.3              
content 1.0               
(29.4 bits)0.8               
0.6               
0.4               
0.2               
0.0
Multilevel AAAATAGCTGCCCAT
consensus T
sequence
NAME STRAND START P-VALUE    SITES 
X00371+3366.74e-10 CACCTGCCCTAAAATAGCTTCCCATGTGAGGGCTA
extracted09+2931.43e-09 CACTTGCCCCAAAATAGCTGCCCATGTGAGGGCCA

Motif 7 block diagrams

NameLowest
p-value
   Motifs
X00371 6.7e-10

+7
extracted09 1.4e-09

+7
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 7 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 7 position-specific scoring matrix


Motif 7 position-specific probability matrix


to known motifs in JASPAR database.





Time  2.23 secs.


P N
MOTIF 8     width = 11     sites = 4     llr = 51     E-value = 4.3e+004

SimplifiedA::3:8::::3:
pos.-specificCaa8a:aa8a8:
probabilityG:::::::::::
matrixT::::3::3::a
bits 2.1 
1.9       
1.7       
1.5       
Information 1.3        
content 1.0           
(18.3 bits)0.8           
0.6           
0.4           
0.2           
0.0
Multilevel CCCCACCCCCT
consensus ATTA
sequence
NAME STRAND START P-VALUE    SITES 
extracted09+2403.54e-07 GCTTCCCCCTCCCCACCCCCTACTGCCCCAA
X00371+2833.54e-07 CGCACAACCACCCCACCCCCTGTGGCCTGAG
danRer3_refGene_NM_20058-3711.30e-06 GAAATGTTAACCACACCCCCTTCCATTTACC
galGal2_xenoRefGene_NM_2-3904.52e-06 GGTTTTATAGCCCCTCCTCATAGACCTACAC

Motif 8 block diagrams

NameLowest
p-value
   Motifs
extracted09 3.5e-07

+8
X00371 3.5e-07

+8
danRer3_refGene_NM_20058 1.3e-06

-8
galGal2_xenoRefGene_NM_2 4.5e-06

-8
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 8 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 8 position-specific scoring matrix


Motif 8 position-specific probability matrix


to known motifs in JASPAR database.





Time  2.54 secs.


P N
MOTIF 9     width = 15     sites = 4     llr = 61     E-value = 4.3e+004

SimplifiedA:::3:::3:5::3::
pos.-specificC::33::::::35:::
probabilityGa:8:a:a3a:83::a
matrixT:a:5:a:5:5:38a:
bits 2.1   
1.9        
1.7        
1.5        
Information 1.3         
content 1.0            
(22.0 bits)0.8            
0.6              
0.4               
0.2               
0.0
Multilevel GTGTGTGTGAGCTTG
consensus CAATCGA
sequence CGT
NAME STRAND START P-VALUE    SITES 
danRer3_refGene_NM_20058+3153.63e-09 GTGTGTGTGTGTGTGTGTGTGTTTGACTGTAAGTG
extracted09-201.95e-08 TATTTAATACGTGTGTGTGTGCATGTACATGTACG
X00371+709.89e-08 GGGGCAGAAGGTGCGTGAGAGGTTGCGAATGGCAG
galGal2_xenoRefGene_NM_2+1513.26e-07 GCTTGACACTGTCAGTGGGACCTTGGGAAGCCAGG

Motif 9 block diagrams

NameLowest
p-value
   Motifs
danRer3_refGene_NM_20058 3.6e-09

+9
extracted09 2e-08

-9
X00371 9.9e-08

+9
galGal2_xenoRefGene_NM_2 3.3e-07

+9
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 9 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 9 position-specific scoring matrix


Motif 9 position-specific probability matrix


to known motifs in JASPAR database.





Time  2.84 secs.


P N
MOTIF 10     width = 11     sites = 4     llr = 50     E-value = 2.1e+004

SimplifiedA3::835:a:::
pos.-specificC:aa::3a::::
probabilityG::::83::a:a
matrixT8::3:::::a:
bits 2.1  
1.9       
1.7       
1.5       
Information 1.3         
content 1.0          
(18.0 bits)0.8          
0.6          
0.4           
0.2           
0.0
Multilevel TCCAGACAGTG
consensus ATAC
sequence G
NAME STRAND START P-VALUE    SITES 
extracted09+2112.48e-07 CTTGTGCAAGTCCAGACAGTGACCTGGCTGC
X00371+2362.48e-07 GCTATGAGAGTCCAGACAGTGCCCAACCTCC
galGal2_xenoRefGene_NM_2+1823.14e-06 CAGGACAGGCTCCTGGCAGTGCGTTTGGGCA
danRer3_refGene_NM_20058+2414.82e-06 GTTCACAAAAACCAACCAGTGTGTATGAGTG

Motif 10 block diagrams

NameLowest
p-value
   Motifs
extracted09 2.5e-07

+10
X00371 2.5e-07

+10
galGal2_xenoRefGene_NM_2 3.1e-06

+10
danRer3_refGene_NM_20058 4.8e-06

+10
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 10 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 10 position-specific scoring matrix


Motif 10 position-specific probability matrix


to known motifs in JASPAR database.





Time  3.12 secs.


P N
MOTIF 11     width = 13     sites = 4     llr = 56     E-value = 1.7e+004

SimplifiedA:::8:a:338:8:
pos.-specificC::::a::8:::33
probabilityGaaa:::a:5:a::
matrixT:::3::::33::8
bits 2.1 
1.9       
1.7       
1.5       
Information 1.3           
content 1.0            
(20.3 bits)0.8            
0.6            
0.4             
0.2             
0.0
Multilevel GGGACAGCGAGAT
consensus TAATCC
sequence T
NAME STRAND START P-VALUE    SITES 
danRer3_refGene_NM_20058+4049.86e-08 GACACGCAGAGGGACAGCGTGATTGACAGGCTG
galGal2_xenoRefGene_NM_2-4751.65e-07 ACCGGTGGCTGGGACAGATAGATAGGTCTCAAG
extracted09+842.27e-07 AGACTTCTAGGGGTCAGCAAGATGCCTGTGCCC
X00371+4244.80e-07 GCAGGGGAGGGGGACAGCGAGCCATTGAGCGAT

Motif 11 block diagrams

NameLowest
p-value
   Motifs
danRer3_refGene_NM_20058 9.9e-08

+11
galGal2_xenoRefGene_NM_2 1.7e-07

-11
extracted09 2.3e-07

+11
X00371 4.8e-07

+11
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 11 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 11 position-specific scoring matrix


Motif 11 position-specific probability matrix


to known motifs in JASPAR database.





Time  3.40 secs.


P N
MOTIF 12     width = 11     sites = 2     llr = 31     E-value = 5.7e+004

SimplifiedA:::::::::a:
pos.-specificC::::::::a::
probabilityG::aaa:::::a
matrixTaa:::aaa:::
bits 2.1      
1.9           
1.7           
1.5           
Information 1.3           
content 1.0           
(22.1 bits)0.8           
0.6           
0.4           
0.2           
0.0
Multilevel TTGGGTTTCAG
consensus
sequence
NAME STRAND START P-VALUE    SITES 
extracted09+1562.20e-07 AGGGGGAGAATTGGGTTTCAGCTGCTGGCAG
X00371+1782.20e-07 GCAGGGAGCGTTGGGTTTCAGGCTGCTGGCG

Motif 12 block diagrams

NameLowest
p-value
   Motifs
extracted09 2.2e-07

+12
X00371 2.2e-07

+12
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 12 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 12 position-specific scoring matrix


Motif 12 position-specific probability matrix


to known motifs in JASPAR database.





Time  3.66 secs.


P N
MOTIF 13     width = 7     sites = 2     llr = 20     E-value = 5.8e+004

SimplifiedAaaa:aaa
pos.-specificC:::a:::
probabilityG:::::::
matrixT:::::::
bits 2.1      
1.9       
1.7       
1.5       
Information 1.3       
content 1.0       
(14.4 bits)0.8       
0.6       
0.4       
0.2       
0.0
Multilevel AAACAAA
consensus
sequence
NAME STRAND START P-VALUE    SITES 
danRer3_refGene_NM_20058-2684.48e-05 TTTCTGAGTCAAACAAACACACACACT
extracted09+444.48e-05 CGTATTAAATAAACAAAAGCAGTCAGA

Motif 13 block diagrams

NameLowest
p-value
   Motifs
danRer3_refGene_NM_20058 4.5e-05

-13
extracted09 4.5e-05

+13
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 13 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 13 position-specific scoring matrix


Motif 13 position-specific probability matrix


to known motifs in JASPAR database.





Time  3.92 secs.


P N
MOTIF 14     width = 13     sites = 2     llr = 34     E-value = 7.8e+004

SimplifiedA::a:aaa55:a:a
pos.-specificC:a:::::::::::
probabilityG:::a:::5:a:a:
matrixTa:::::::5::::
bits 2.1       
1.9           
1.7           
1.5           
Information 1.3           
content 1.0             
(24.4 bits)0.8             
0.6             
0.4             
0.2             
0.0
Multilevel TCAGAAAAAGAGA
consensus GT
sequence
NAME STRAND START P-VALUE    SITES 
danRer3_refGene_NM_20058+2782.16e-08 TTTGTTTGACTCAGAAAAAGAGAGCGAGGGAGT
extracted09+564.60e-08 ACAAAAGCAGTCAGAAAGTGAGAGGAGGAGACT

Motif 14 block diagrams

NameLowest
p-value
   Motifs
danRer3_refGene_NM_20058 2.2e-08

+14
extracted09 4.6e-08

+14
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 14 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 14 position-specific scoring matrix


Motif 14 position-specific probability matrix


to known motifs in JASPAR database.





Time  4.19 secs.


P N
MOTIF 15     width = 8     sites = 2     llr = 22     E-value = 9.5e+004

SimplifiedA::::::::
pos.-specificC:a:aa:::
probabilityG::::::::
matrixTa:a::aaa
bits 2.1     
1.9        
1.7        
1.5        
Information 1.3        
content 1.0        
(16.2 bits)0.8        
0.6        
0.4        
0.2        
0.0
Multilevel TCTCCTTT
consensus
sequence
NAME STRAND START P-VALUE    SITES 
galGal2_xenoRefGene_NM_2-381.34e-05 TCCTCACGCCTCTCCTTTCCCTGCACTG
extracted09+4731.34e-05 GCCCACACTCTCTCCTTTTGTCCTCTTT

Motif 15 block diagrams

NameLowest
p-value
   Motifs
galGal2_xenoRefGene_NM_2 1.3e-05

-15
extracted09 1.3e-05

+15
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 15 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 15 position-specific scoring matrix


Motif 15 position-specific probability matrix


to known motifs in JASPAR database.





Time  4.44 secs.


P N
MOTIF 16     width = 10     sites = 2     llr = 27     E-value = 1.1e+005

SimplifiedA::5:::aa::
pos.-specificC:::::a:::a
probabilityG:::a::::a:
matrixTaa5:a:::::
bits 2.1     
1.9         
1.7         
1.5         
Information 1.3         
content 1.0          
(19.2 bits)0.8          
0.6          
0.4          
0.2          
0.0
Multilevel TTAGTCAAGC
consensus T
sequence
NAME STRAND START P-VALUE    SITES 
galGal2_xenoRefGene_NM_2+3331.66e-06 GGCTGATTAGTTAGTCAAGCCTGAAAGGGA
X00371+4481.66e-06 TTGAGCGATCTTTGTCAAGCATCCCAGAAG

Motif 16 block diagrams

NameLowest
p-value
   Motifs
galGal2_xenoRefGene_NM_2 1.7e-06

+16
X00371 1.7e-06

+16
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 16 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 16 position-specific scoring matrix


Motif 16 position-specific probability matrix


to known motifs in JASPAR database.





Time  4.69 secs.


P N
MOTIF 17     width = 8     sites = 2     llr = 22     E-value = 1.5e+005

SimplifiedA::::::::
pos.-specificC::aa:a::
probabilityGa:::::::
matrixT:a::a:aa
bits 2.1    
1.9        
1.7        
1.5        
Information 1.3        
content 1.0        
(16.0 bits)0.8        
0.6        
0.4        
0.2        
0.0
Multilevel GTCCTCTT
consensus
sequence
NAME STRAND START P-VALUE    SITES 
extracted09+4821.50e-05 CTCTCCTTTTGTCCTCTTTAGAAGCCAC
X00371+1471.50e-05 AACATGACAGGTCCTCTTGGGAGGGCTG

Motif 17 block diagrams

NameLowest
p-value
   Motifs
extracted09 1.5e-05

+17
X00371 1.5e-05

+17
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 17 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 17 position-specific scoring matrix


Motif 17 position-specific probability matrix


to known motifs in JASPAR database.





Time  4.94 secs.


P N
MOTIF 18     width = 8     sites = 2     llr = 22     E-value = 1.5e+005

SimplifiedA::a::::a
pos.-specificC:::aaaa:
probabilityG::::::::
matrixTaa::::::
bits 2.1    
1.9        
1.7        
1.5        
Information 1.3        
content 1.0        
(16.0 bits)0.8        
0.6        
0.4        
0.2        
0.0
Multilevel TTACCCCA
consensus
sequence
NAME STRAND START P-VALUE    SITES 
danRer3_refGene_NM_20058-3581.50e-05 CCCCTTCCATTTACCCCATCAGAACACA
galGal2_xenoRefGene_NM_2+221.50e-05 TTGAAAGACCTTACCCCAGTGCAGGGAA

Motif 18 block diagrams

NameLowest
p-value
   Motifs
danRer3_refGene_NM_20058 1.5e-05

-18
galGal2_xenoRefGene_NM_2 1.5e-05

+18
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 18 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 18 position-specific scoring matrix


Motif 18 position-specific probability matrix


to known motifs in JASPAR database.





Time  5.20 secs.


P N
MOTIF 19     width = 6     sites = 2     llr = 17     E-value = 1.5e+005

SimplifiedA:::aa:
pos.-specificC::::::
probabilityG:aa:::
matrixTa::::a
bits 2.1    
1.9      
1.7      
1.5      
Information 1.3      
content 1.0      
(12.2 bits)0.8      
0.6      
0.4      
0.2      
0.0
Multilevel TGGAAT
consensus
sequence
NAME STRAND START P-VALUE    SITES 
danRer3_refGene_NM_20058+2162.15e-04 CAGTACGCTATGGAATGTCCCCACAG
galGal2_xenoRefGene_NM_2+1222.15e-04 CGTGCTCTTCTGGAATCTCCTGCTGC

Motif 19 block diagrams

NameLowest
p-value
   Motifs
danRer3_refGene_NM_20058 0.00021

+19
galGal2_xenoRefGene_NM_2 0.00021

+19
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 19 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 19 position-specific scoring matrix


Motif 19 position-specific probability matrix


to known motifs in JASPAR database.





Time  5.45 secs.


P N
MOTIF 20     width = 15     sites = 2     llr = 39     E-value = 2.1e+005

SimplifiedAa::a:::5:::::aa
pos.-specificC:aa:::5::aa:a::
probabilityG::::aa:5a::::::
matrixT::::::5::::a:::
bits 2.1     
1.9             
1.7             
1.5             
Information 1.3             
content 1.0               
(27.8 bits)0.8               
0.6               
0.4               
0.2               
0.0
Multilevel ACCAGGCAGCCTCAA
consensus TG
sequence
NAME STRAND START P-VALUE    SITES 
extracted09+4313.13e-09 GCCCTTCAGGACCAGGTGGCCTCAAATCTCAGCTG
X00371+4873.13e-09 CGCCCTTGGGACCAGGCAGCCTCAA

Motif 20 block diagrams

NameLowest
p-value
   Motifs
extracted09 3.1e-09

+20
X00371 3.1e-09

+20
SCALE
| | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475

Motif 20 in BLOCKS format


to BLOCKS multiple alignment processor.
Motif 20 position-specific scoring matrix


Motif 20 position-specific probability matrix


to known motifs in JASPAR database.





Time  5.70 secs.


P N
SUMMARY OF MOTIFS


Combined block diagrams: non-overlapping sites with p-value < 0.0001

NameCombined
p-value
   Motifs
X00371 5.29e-41

+9
+3
+17
+12
+2
+10 +8
+8
+1
+7
+4
-6
+11
+16
+5
+20
extracted09 7.92e-47
+6
-9
+13
+14
+11
+3
+12
+10
+2
+10
+8
+1
+7
+4
+5
+20
+15
+17
galGal2_xenoRefGene_NM_2 3.20e-27

+18
-15
+9
+10
+2
+4
+1
+3
+16
-6
-8
+5
-11
danRer3_refGene_NM_20058 9.10e-25

-3
-1
+4
+2
+9
+9
-6
+9
+10
+9
+14
+9
+9
-18
-8
+11
+5
SCALE
| | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575

Motif summary in machine readable format.
Stopped because nmotifs = 20 reached.


CPU: unknown


EXPLANATION OF MEME RESULTS

The MEME results consist of:

MOTIFS

For each motif that it discovers in the training set, MEME prints the following information:


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