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meme.out
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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.5.7 (Release date: 2007-12-17 16:56:19 -0800 (Mon, 17 Dec 2007))
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= test.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
SEQ1; 1.0000 200 SEQ2; 1.0000 200
SEQ3; 1.0000 200 SEQ4; 1.0000 200
SEQ5; 1.0000 200 SEQ6; 1.0000 200
SEQ7; 1.0000 200 SEQ8; 1.0000 200
SEQ9; 1.0000 200 SEQ10; 1.0000 200
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme test.fa -dna -w 10 -dir /home/bartek/MetaMotif/meme
model: mod= zoops nmotifs= 1 evt= inf
object function= E-value of product of p-values
width: minw= 10 maxw= 10 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 2 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 2000 N= 10
strands: +
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.255 C 0.235 G 0.261 T 0.249
Background letter frequencies (from dataset with add-one prior applied):
A 0.255 C 0.236 G 0.260 T 0.249
********************************************************************************
********************************************************************************
MOTIF 1 width = 10 sites = 10 llr = 140 E-value = 1.1e-022
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::aa::::a
pos.-specific C a:a:::a:::
probability G :::::::a::
matrix T :a:::a::a:
bits 2.1 *** ** *
1.9 **********
1.7 **********
1.5 **********
Information 1.3 **********
content 1.0 **********
(20.1 bits) 0.8 **********
0.6 **********
0.4 **********
0.2 **********
0.0 ----------
Multilevel CTCAATCGTA
consensus
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Start P-value Site
------------- ----- --------- ----------
SEQ10; 3 8.71e-07 TT CTCAATCGTA GAGTATGCTT
SEQ9; 93 8.71e-07 CGCCTAGAAA CTCAATCGTA GAGTATCACG
SEQ8; 172 8.71e-07 CCCGGAGTAT CTCAATCGTA GATGAATACC
SEQ7; 177 8.71e-07 AAGTCTTTGA CTCAATCGTA GACCCAACAC
SEQ6; 105 8.71e-07 GTCAGCCGGT CTCAATCGTA GATCAGAGGC
SEQ5; 185 8.71e-07 ACGGGCAAGC CTCAATCGTA GAGGAT
SEQ4; 173 8.71e-07 GTTCGAGAGC CTCAATCGTA GATAACCTCT
SEQ3; 112 8.71e-07 GTTATATTGG CTCAATCGTA GATGAAACCA
SEQ2; 172 8.71e-07 AAGCGTCGTG CTCAATCGTA GATAACAGAG
SEQ1; 52 8.71e-07 CTTTACTCGG CTCAATCGTA GAGGCGGTGC
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SEQ10; 8.7e-07 2_[1]_188
SEQ9; 8.7e-07 92_[1]_98
SEQ8; 8.7e-07 171_[1]_19
SEQ7; 8.7e-07 176_[1]_14
SEQ6; 8.7e-07 104_[1]_86
SEQ5; 8.7e-07 184_[1]_6
SEQ4; 8.7e-07 172_[1]_18
SEQ3; 8.7e-07 111_[1]_79
SEQ2; 8.7e-07 171_[1]_19
SEQ1; 8.7e-07 51_[1]_139
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=10 seqs=10
SEQ10; ( 3) CTCAATCGTA 1
SEQ9; ( 93) CTCAATCGTA 1
SEQ8; ( 172) CTCAATCGTA 1
SEQ7; ( 177) CTCAATCGTA 1
SEQ6; ( 105) CTCAATCGTA 1
SEQ5; ( 185) CTCAATCGTA 1
SEQ4; ( 173) CTCAATCGTA 1
SEQ3; ( 112) CTCAATCGTA 1
SEQ2; ( 172) CTCAATCGTA 1
SEQ1; ( 52) CTCAATCGTA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 10 n= 1910 bayes= 8.51691 E= 1.1e-022
-997 208 -997 -997
-997 -997 -997 200
-997 208 -997 -997
197 -997 -997 -997
197 -997 -997 -997
-997 -997 -997 200
-997 208 -997 -997
-997 -997 194 -997
-997 -997 -997 200
197 -997 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 10 nsites= 10 E= 1.1e-022
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 0.000000 1.000000
1.000000 0.000000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
CTCAATCGTA
--------------------------------------------------------------------------------
Time 0.26 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
SEQ1; 1.66e-04 51_[1(8.71e-07)]_139
SEQ2; 1.66e-04 171_[1(8.71e-07)]_19
SEQ3; 1.66e-04 111_[1(8.71e-07)]_79
SEQ4; 1.66e-04 172_[1(8.71e-07)]_18
SEQ5; 1.66e-04 184_[1(8.71e-07)]_6
SEQ6; 1.66e-04 104_[1(8.71e-07)]_86
SEQ7; 1.66e-04 176_[1(8.71e-07)]_14
SEQ8; 1.66e-04 171_[1(8.71e-07)]_19
SEQ9; 1.66e-04 92_[1(8.71e-07)]_98
SEQ10; 1.66e-04 2_[1(8.71e-07)]_188
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 1 reached.
********************************************************************************
CPU: pc-arendt9
********************************************************************************