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mgalardini/meme.txt

Created January 13, 2015 17:54
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Meme motif file that makes Bio.motifs.read crash
Raw
meme.txt
********************************************************************************
MEME - Motif discovery tool
********************************************************************************
MEME version 4.10.0 (Release date: Wed May 21 10:35:36 2014 +1000)
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= seqs.fa
ALPHABET= ACGT
Sequence name Weight Length Sequence name Weight Length
------------- ------ ------ ------------- ------ ------
1 1.0000 22 2 1.0000 30
3 1.0000 30 4 1.0000 30
5 1.0000 30 6 1.0000 26
7 1.0000 29 8 1.0000 30
9 1.0000 30 10 1.0000 30
********************************************************************************
********************************************************************************
COMMAND LINE SUMMARY
********************************************************************************
This information can also be useful in the event you wish to report a
problem with the MEME software.
command: meme seqs.fa -dna -oc . -nostatus -time 18000 -maxsize 60000 -mod oops -nmotifs 1 -minw 23 -maxw 50 -revcomp
model: mod= oops nmotifs= 1 evt= inf
object function= E-value of product of p-values
width: minw= 22 maxw= 22 minic= 0.00
width: wg= 11 ws= 1 endgaps= yes
nsites: minsites= 10 maxsites= 10 wnsites= 0.8
theta: prob= 1 spmap= uni spfuzz= 0.5
global: substring= yes branching= no wbranch= no
em: prior= dirichlet b= 0.01 maxiter= 50
distance= 1e-05
data: n= 287 N= 10
strands: + -
sample: seed= 0 seqfrac= 1
Letter frequencies in dataset:
A 0.265 C 0.235 G 0.235 T 0.265
Background letter frequencies (from dataset with add-one prior applied):
A 0.265 C 0.235 G 0.235 T 0.265
********************************************************************************
********************************************************************************
MOTIF 1 MEME width = 22 sites = 10 llr = 173 E-value = 1.1e-030
********************************************************************************
--------------------------------------------------------------------------------
Motif 1 Description
--------------------------------------------------------------------------------
Simplified A 3241423:::9a::1:9:a:38
pos.-specific C 31331:2a:a::19:::::122
probability G 2513263::::::19::a:44:
matrix T 2223322:a:1:9::a1::51:
bits 2.1 * * *
1.9 *** * * **
1.7 *** * *** **
1.5 ************
Relative 1.3 ************ *
Entropy 1.0 ************ *
(24.9 bits) 0.8 ************ *
0.6 * ************* *
0.4 * ************* *
0.2 ***** ***************
0.0 ----------------------
Multilevel AGACAGACTCAATCGTAGATGA
consensus CACGTAG GAC
sequence GTTTGTC C
T T
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name Strand Start P-value Site
------------- ------ ----- --------- ----------------------
7 + 3 1.41e-11 TT CGAGAGCCTCAATCGTAGATAA CCTCT
8 + 4 1.25e-10 GTT ATATTGGCTCAATCGTAGATGA AACCA
5 + 4 2.85e-10 GTC AGCCGGTCTCAATCGTAGATCA GAGGC
6 + 4 3.83e-10 ACG GGCAAGCCTCAATCGTAGAGGA T
3 + 4 5.83e-10 CCC GGAGTATCTCAATCGTAGATGA ATACC
9 + 4 1.08e-09 AAG CGTCGTGCTCAATCGTAGATAA CAGAG
2 + 4 4.21e-09 CGC CTAGAAACTCAATCGTAGAGTA TCACG
10 + 4 7.76e-09 CTT TACTCGGCTCAATCGTAGAGGC GGTGC
4 + 4 5.28e-08 AAG TCTTTGACTCAATCGTAGACCC AACAC
1 - 1 2.41e-06 . AAGCATACTCTACGATTGAGAA
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME POSITION P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
7 1.4e-11 2_[+1]_5
8 1.3e-10 3_[+1]_5
5 2.8e-10 3_[+1]_5
6 3.8e-10 3_[+1]_1
3 5.8e-10 3_[+1]_5
9 1.1e-09 3_[+1]_5
2 4.2e-09 3_[+1]_5
10 7.8e-09 3_[+1]_5
4 5.3e-08 3_[+1]_5
1 2.4e-06 [-1]
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL MOTIF 1 width=22 seqs=10
7 ( 3) CGAGAGCCTCAATCGTAGATAA 1
8 ( 4) ATATTGGCTCAATCGTAGATGA 1
5 ( 4) AGCCGGTCTCAATCGTAGATCA 1
6 ( 4) GGCAAGCCTCAATCGTAGAGGA 1
3 ( 4) GGAGTATCTCAATCGTAGATGA 1
9 ( 4) CGTCGTGCTCAATCGTAGATAA 1
2 ( 4) CTAGAAACTCAATCGTAGAGTA 1
10 ( 4) TACTCGGCTCAATCGTAGAGGC 1
4 ( 4) TCTTTGACTCAATCGTAGACCC 1
1 ( 1) AAGCATACTCTACGATTGAGAA 1
//
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 22 n= 77 bayes= 2.74416 E= 1.1e-030
18 35 -23 -40
-40 -123 109 -40
60 35 -123 -40
-140 35 35 18
60 -123 -23 18
-40 -997 135 -40
18 -23 35 -40
-997 209 -997 -997
-997 -997 -997 192
-997 209 -997 -997
177 -997 -997 -140
192 -997 -997 -997
-997 -123 -997 177
-997 193 -123 -997
-140 -997 193 -997
-997 -997 -997 192
177 -997 -997 -140
-997 -997 209 -997
192 -997 -997 -997
-997 -123 76 92
18 -23 76 -140
160 -23 -997 -997
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 22 nsites= 10 E= 1.1e-030
0.300000 0.300000 0.200000 0.200000
0.200000 0.100000 0.500000 0.200000
0.400000 0.300000 0.100000 0.200000
0.100000 0.300000 0.300000 0.300000
0.400000 0.100000 0.200000 0.300000
0.200000 0.000000 0.600000 0.200000
0.300000 0.200000 0.300000 0.200000
0.000000 1.000000 0.000000 0.000000
0.000000 0.000000 0.000000 1.000000
0.000000 1.000000 0.000000 0.000000
0.900000 0.000000 0.000000 0.100000
1.000000 0.000000 0.000000 0.000000
0.000000 0.100000 0.000000 0.900000
0.000000 0.900000 0.100000 0.000000
0.100000 0.000000 0.900000 0.000000
0.000000 0.000000 0.000000 1.000000
0.900000 0.000000 0.000000 0.100000
0.000000 0.000000 1.000000 0.000000
1.000000 0.000000 0.000000 0.000000
0.000000 0.100000 0.400000 0.500000
0.300000 0.200000 0.400000 0.100000
0.800000 0.200000 0.000000 0.000000
--------------------------------------------------------------------------------
--------------------------------------------------------------------------------
Motif 1 regular expression
--------------------------------------------------------------------------------
[ACGT][GAT][ACT][CGT][ATG][GAT][AGCT]CTCAATCGTAGA[TG][GAC][AC]
--------------------------------------------------------------------------------
Time 0.02 secs.
********************************************************************************
********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************
--------------------------------------------------------------------------------
Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME COMBINED P-VALUE MOTIF DIAGRAM
------------- ---------------- -------------
1 4.82e-06 [-1(2.41e-06)]
2 7.57e-08 3_[+1(4.21e-09)]_5
3 1.05e-08 3_[+1(5.83e-10)]_5
4 9.50e-07 3_[+1(5.28e-08)]_5
5 5.12e-09 3_[+1(2.85e-10)]_5
6 3.83e-09 3_[+1(3.83e-10)]_1
7 2.25e-10 2_[+1(1.41e-11)]_5
8 2.25e-09 3_[+1(1.25e-10)]_5
9 1.94e-08 3_[+1(1.08e-09)]_5
10 1.40e-07 3_[+1(7.76e-09)]_5
--------------------------------------------------------------------------------
********************************************************************************
********************************************************************************
Stopped because nmotifs = 1 reached.
********************************************************************************
CPU: my-computer
********************************************************************************
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