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 3.0 (Release date: 2002/04/02 00:11:59)

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

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.sdsc.edu.


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= 71NTCA.NT
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
71C_2335094-2335693c     1.0000    600  71C_2807124-2807482d     1.0000    359  
71C_704034-704678d       1.0000    645  71C_701219-701460c       1.0000    242  
NC_4477940-4478869d      1.0000    930  71C_3427135-3428063d     1.0000    929  


COMMAND LINE SUMMARY

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

command: meme 71NTCA.NT -nmotifs 3 -dna 

model:  mod=         zoops    nmotifs=         3    evt=           inf
object function=  E-value of product of p-values
width:  minw=            8    maxw=           50    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=        6    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=            3705    N=               6
strands: +
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.328 C 0.175 G 0.174 T 0.322 
Background letter frequencies (from dataset with add-one prior applied):
A 0.328 C 0.176 G 0.174 T 0.322 


P N
MOTIF 1
    width = 10     sites = 6     llr = 66     E-value = 5.3e+001

SimplifiedA335:2:::82
pos.-specificC:7::2::a::
probabilityG7::::aa:28
matrixT::5a7:::::
.
bits 2.5   
2.3   
2.0   
1.8    
Information 1.5     
content 1.3       
(15.8 bits)1.0        
0.8        
0.5          
0.3          
0.0
.
Multilevel GCATTGGCAG
consensus AAT
sequence
.
NAME   START P-VALUE    SITES
 
71C_2807124-2807482d3086.28e-07 GGGCTTAGATGCTTTGGCAGATTCTGGTTT
71C_2335094-2335693c2256.28e-07 CGAACAAGCAGCATTGGCAGAATACGGTTA
71C_3427135-3428063d8213.66e-06 TTTAAAAGATACATTGGCAGTACATTAAAA
71C_701219-701460c1141.32e-05 CCTTTTAAGAGATTAGGCAGGGGAAAATAA
71C_704034-704678d2901.45e-05 CTTCAGTGAAACATCGGCGGCGTGTCAGTC
NC_4477940-4478869d5362.19e-05 AAGAAATCTGGATTTGGCAAGGGTTTCTAG


Motif 1 block diagrams

NameLowest
p-value
   Motifs
71C_2807124-2807482d 6.3e-07

1
71C_2335094-2335693c 6.3e-07

1
71C_3427135-3428063d 3.7e-06

1
71C_701219-701460c 1.3e-05

1
71C_704034-704678d 1.4e-05

1
NC_4477940-4478869d 2.2e-05

1
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900


Motif 1 in BLOCKS format


to BLOCKS multiple alignment processor.


Motif 1 position-specific scoring matrix


Motif 1 position-specific probability matrix






Time 24.93 secs.


P N
MOTIF 2
    width = 50     sites = 4     llr = 155     E-value = 7.7e+001

SimplifiedA::::33a3::::5533335::353:558:3::335::5a53::5:5:55:
pos.-specificC85aa85:388853:3585353:5333::3::::333a:::5:a555:33a
probabilityG:5:::::5::3:::::::::53:333::5:aa5538:3:3:3::5:::::
matrixT3::::3::33:53553:33535:35:5338::3::::3:338::::a33:
.
bits 2.5       
2.3       
2.0       
1.8         
Information 1.5                   
content 1.3                   
(56.0 bits)1.0                         
0.8                               
0.5                                         
0.3                                                 
0.0
.
Multilevel CCCCCCAGCCCCAATCCCACGTAATAAAGTGGGGAGCAAACTCACATAAC
consensus TGAAATTGTCTAAAACTCACCCCTTCAAACCGGAGCGCCC
sequence TCTCTTTTGGGGTTCGTTTTT
T
.
NAME   START P-VALUE    SITES
 
71C_704034-704678d4206.38e-23 AAAAACCTTACCCCCCAGCCCCCTTCCCTTGTAGGGAAGTGGGAGCCAAACTCCCCTCTCCGCGTCGGAG
71C_2335094-2335693c3422.53e-18 AAAATTGTCTCGCCCCAACCCTAAATCTACGACATATAGAGGAGCGCTAGTTCAGATACCTGTTAGGTCA
NC_4477940-4478869d1064.08e-18 AACTACACTGCCCCCTACTCCCTTTCCCCCTGCTTCTTCTGGTCAGCGATCGCCCATTACTCCTTCAATC
71C_701219-701460c1541.83e-16 TTGTGTTAATTGCCAAAGCTGTAACAAAATCTACCAAATTGGGGAGCAAAATCAGCTAACTTAATTGAAT


Motif 2 block diagrams

NameLowest
p-value
   Motifs
71C_704034-704678d 6.4e-23

2
71C_2335094-2335693c 2.5e-18

2
NC_4477940-4478869d 4.1e-18

2
71C_701219-701460c 1.8e-16

2
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900


Motif 2 in BLOCKS format


to BLOCKS multiple alignment processor.


Motif 2 position-specific scoring matrix


Motif 2 position-specific probability matrix






Time 48.74 secs.


P N
MOTIF 3
    width = 8     sites = 6     llr = 57     E-value = 2.9e+002

SimplifiedA::33a:::
pos.-specificC:87:::::
probabilityGa::7::a2
matrixT:2:::a:8
.
bits 2.5  
2.3  
2.0  
1.8   
Information 1.5     
content 1.3       
(13.7 bits)1.0        
0.8        
0.5        
0.3        
0.0
.
Multilevel GCCGATGT
consensus AA
sequence
.
NAME   START P-VALUE    SITES
 
71C_3427135-3428063d8425.54e-06 ACATTAAAATGCCGATGTTAGATAAATT
NC_4477940-4478869d6855.54e-06 TCAACGTCAAGCCGATGTTGTTTTTCTT
71C_704034-704678d2322.94e-05 GACAAATTTAGCCAATGTAAAAGACTAC
71C_2807124-2807482d1722.94e-05 TCCCTTTTGTGCAGATGTCGAAAGAAAG
71C_2335094-2335693c215.08e-05 CAGTTATTGAGCCAATGGGGTGTCCGAA
71C_701219-701460c781.25e-04 TCATACTACTGTAGATGTACTTCACCCT


Motif 3 block diagrams

NameLowest
p-value
   Motifs
71C_3427135-3428063d 5.5e-06

3
NC_4477940-4478869d 5.5e-06

3
71C_704034-704678d 2.9e-05

3
71C_2807124-2807482d 2.9e-05

3
71C_2335094-2335693c 5.1e-05

3
71C_701219-701460c 0.00012

3
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900


Motif 3 in BLOCKS format


to BLOCKS multiple alignment processor.


Motif 3 position-specific scoring matrix


Motif 3 position-specific probability matrix






Time 69.88 secs.


P N
SUMMARY OF MOTIFS



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

NameCombined
p-value
   Motifs
71C_2335094-2335693c 1.67e-17

3
1
2
71C_2807124-2807482d 2.21e-04

3
1
1
71C_704034-704678d 9.57e-21

3
1
2
71C_701219-701460c 2.66e-15

1
2
NC_4477940-4478869d 3.46e-16

2
1
3
71C_3427135-3428063d 1.19e-03

3
1
3
SCALE
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
1 25 50 75 100 125 150 175 200 225 250 275 300 325 350 375 400 425 450 475 500 525 550 575 600 625 650 675 700 725 750 775 800 825 850 875 900 925

Motif summary in machine readable format.


Stopped because nmotifs = 3 reached.


CPU: hercules.vcu.edu


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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