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********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 3.0 (Release date: 2004/08/18 09:07:01)
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= INO_up800.s
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
CHO1 1.0000 800 CHO2 1.0000 800
FAS1 1.0000 800 FAS2 1.0000 800
ACC1 1.0000 800 INO1 1.0000 800
OPI3 1.0000 800
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme -mod oops -dna -revcomp -nmotifs 2 -bfile yeast.nc.6.freq INO_up800.s
model: mod= oops nmotifs= 2 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= 7 maxsites= 7 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 5600 N= 7
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.304 C 0.196 G 0.196 T 0.304
Background letter frequencies (from yeast.nc.6.freq):
A 0.324 C 0.176 G 0.176 T 0.324
********************************************************************************
********************************************************************************
MOTIF 1 width = 12 sites = 7 llr = 95 E-value = 2.0e-001
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A :::9:a::::3:
pos.-specific C ::a:9:11691a
probability G ::::1::94:4:
matrix T aa:1::9::11:
bits 2.5 * *
2.3 * *
2.0 * * * *
1.8 * * * * *
Information 1.5 *** ** *** *
content 1.3 *** ****** *
(19.5 bits) 1.0 ********** *
0.8 ********** *
0.5 ********** *
0.3 ************
0.0 ------------
Multilevel TTCACATGCCGC
consensus G A
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ------------
INO1 - 620 1.85e-08 GACAATACTT TTCACATGCCGC ATTTAGCCGC
FAS1 + 95 1.85e-08 GGCCAAAAAC TTCACATGCCGC CCAGCCAAGC
ACC1 + 83 1.52e-07 CGTTAAAATC TTCACATGGCCC GGCCGCGCGC
CHO2 + 354 2.52e-07 TGCCACACTT TTCTCATGCCGC ATTCATTATT
CHO1 + 611 4.23e-07 ACTTTGAACG TTCACACGGCAC CCTCACGCCT
FAS2 + 567 9.43e-07 CTCCCGCGTT TTCACATGCTAC CTCATTCGCC
OPI3 + 340 3.32e-06 CCAAGCCTCC TTCAGATCGCTC TTGTCGACCG
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
INO1 1.8e-08 619_[-1]_169
FAS1 1.8e-08 94_[+1]_694
ACC1 1.5e-07 82_[+1]_706
CHO2 2.5e-07 353_[+1]_435
CHO1 4.2e-07 610_[+1]_178
FAS2 9.4e-07 566_[+1]_222
OPI3 3.3e-06 339_[+1]_449
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=12 seqs=7
INO1 ( 620) TTCACATGCCGC 1
FAS1 ( 95) TTCACATGCCGC 1
ACC1 ( 83) TTCACATGGCCC 1
CHO2 ( 354) TTCTCATGCCGC 1
CHO1 ( 611) TTCACACGGCAC 1
FAS2 ( 567) TTCACATGCTAC 1
OPI3 ( 340) TTCAGATCGCTC 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 12 n= 5523 bayes= 9.62205 E= 2.0e-001
-945 -945 -945 162
-945 -945 -945 162
-945 251 -945 -945
140 -945 -945 -118
-945 229 -30 -945
162 -945 -945 -945
-945 -30 -945 140
-945 -30 229 -945
-945 170 129 -945
-945 229 -945 -118
-18 -30 129 -118
-945 251 -945 -945
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 12 nsites= 7 E= 2.0e-001
0.000000 0.000000 0.000000 1.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.857143 0.000000 0.000000 0.142857
0.000000 0.857143 0.142857 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.142857 0.000000 0.857143
0.000000 0.142857 0.857143 0.000000
0.000000 0.571429 0.428571 0.000000
0.000000 0.857143 0.000000 0.142857
0.285714 0.142857 0.428571 0.142857
0.000000 1.000000 0.000000 0.000000
--------------------------------------------------------------------------------
Time 20.91 secs.
********************************************************************************
********************************************************************************
MOTIF 2 width = 10 sites = 7 llr = 81 E-value = 1.1e+002
********************************************************************************
--------------------------------------------------------------------------------
Motif 2 Description
--------------------------------------------------------------------------------
Simplified A ::1:::9:6:
pos.-specific C :a:::a:911
probability G 3:1aa:1:19
matrix T 7:7::::11:
bits 2.5 * ***
2.3 * ***
2.0 * *** *
1.8 * *** * *
Information 1.5 * *** * *
content 1.3 * ***** *
(16.7 bits) 1.0 ** ***** *
0.8 ** ***** *
0.5 ******** *
0.3 **********
0.0 ----------
Multilevel TCTGGCACAG
consensus G
sequence
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ----------
OPI3 - 186 3.24e-07 GAAAACCAGA TCTGGCACAG ACCGTTGTCA
ACC1 + 232 3.24e-07 CCAGTCGTAT TCTGGCACAG TATAGCCTAG
CHO1 - 559 3.24e-07 ATATTCAGTG TCTGGCACAG AAGTCTGCAC
INO1 - 283 5.29e-06 ACGGTCTACG GCGGGCGCAG TCGCATGTCT
FAS1 + 44 6.25e-06 TACACGAGGT GCAGGCACGG TTCACTACTC
FAS2 - 185 8.48e-06 TTCTTGCTTT TCTGGCACTC TTGACGGCTT
CHO2 - 413 8.48e-06 TTTTGCCGTT TCTGGCATCG CCGTTCATTT
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
OPI3 3.2e-07 185_[-2]_605
ACC1 3.2e-07 231_[+2]_559
CHO1 3.2e-07 558_[-2]_232
INO1 5.3e-06 282_[-2]_508
FAS1 6.3e-06 43_[+2]_747
FAS2 8.5e-06 184_[-2]_606
CHO2 8.5e-06 412_[-2]_378
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 2 width=10 seqs=7
OPI3 ( 186) TCTGGCACAG 1
ACC1 ( 232) TCTGGCACAG 1
CHO1 ( 559) TCTGGCACAG 1
INO1 ( 283) GCGGGCGCAG 1
FAS1 ( 44) GCAGGCACGG 1
FAS2 ( 185) TCTGGCACTC 1
CHO2 ( 413) TCTGGCATCG 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 10 n= 5537 bayes= 9.62571 E= 1.1e+002
-945 -945 70 114
-945 251 -945 -945
-118 -945 -30 114
-945 -945 251 -945
-945 -945 251 -945
-945 251 -945 -945
140 -945 -30 -945
-945 229 -945 -118
82 -30 -30 -118
-945 -30 229 -945
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 10 nsites= 7 E= 1.1e+002
0.000000 0.000000 0.285714 0.714286
0.000000 1.000000 0.000000 0.000000
0.142857 0.000000 0.142857 0.714286
0.000000 0.000000 1.000000 0.000000
0.000000 0.000000 1.000000 0.000000
0.000000 1.000000 0.000000 0.000000
0.857143 0.000000 0.142857 0.000000
0.000000 0.857143 0.000000 0.142857
0.571429 0.142857 0.142857 0.142857
0.000000 0.142857 0.857143 0.000000
--------------------------------------------------------------------------------
Time 41.19 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
CHO1 5.44e-06 152_[+2(1.10e-05)]_396_[-2(3.24e-07)]_42_[+1(4.23e-07)]_17_[+1(1.23e-05)]_149
CHO2 6.96e-05 353_[+1(2.52e-07)]_47_[-2(8.48e-06)]_378
FAS1 4.61e-06 43_[+2(6.25e-06)]_41_[+1(1.85e-08)]_694
FAS2 2.34e-04 184_[-2(8.48e-06)]_372_[+1(9.43e-07)]_222
ACC1 2.09e-06 82_[+1(1.52e-07)]_137_[+2(3.24e-07)]_559
INO1 3.95e-06 282_[-2(5.29e-06)]_327_[-1(1.85e-08)]_55_[+1(7.55e-06)]_102
OPI3 3.70e-05 185_[-2(3.24e-07)]_144_[+1(3.32e-06)]_449
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 2 reached.
********************************************************************************
CPU: pmgm2
********************************************************************************
|
