[Bioperl-l] Error when parsing MEME file

Amonida Zadissa amonida at sanger.otago.ac.nz
Thu May 6 03:07:14 EDT 2004


Stefan and Jason,

Thanks for your replies. I was using bioperl-1.4 but now I have
bioperl-live installed. Nevertheless, the problem seems to be there
but I get new warnings complainging about both strands now.

Argument "-" isn't numeric in addition (+) at
/opt/share/perl/5.8.3/Bio/LocatableSeq.pm line 167, <GEN0> line 699.
Argument "+" isn't numeric in addition (+) at
/opt/share/perl/5.8.3/Bio/Matrix/PSM/InstanceSite.pm line 106, <GEN0>
line 700.

Could this depend on my installation (which by the way went fine)?

I'm attaching the MEME test file I have used.

Thanks for any help,
Amonida

On Wed, May 05, 2004 at 02:51:12PM -0400, Stefan Kirov wrote:
> Fixed now, check it from bioperl-live
> Stefan
> 
> Amonida Zadissa wrote:
> 
> >Hi everyone,
> >
> >I'm trying to parse a MEME file using the Bio::Matrix::PSM
> >modules but I'm experiencing problems and was hoping someone on
> >the list could help me.
> >
> >The script is attached below. I get a warning saying the
> >following for each "problematic" instance:
> >
> >Argument "-" isn't numeric in addition (+) at 
> >/opt/share/perl/5.8.3/Bio/Matrix/PSM/InstanceSite.pm line 106, <GEN0> line 
> >1164.
> >
> >Whenever the strand sign is negative the start position is
> >assigned the sign and the score is assigned the start position,
> >so everything seems to shift one column. This happens only
> >if the strand is negative. Note that '$instance' becomes a
> >Bio::Matrix::PSM::InstanceSite object.
> >
> >Is this a parsing error in "InstanceSite.pm" or is my script
> >somehow wrong?
> >
> >Would appreciate any help and by the way thanks for providing this
> >forum!
> >
> >Cheers,
> >Amonida
> >
> >********************************************************************
> >#!/usr/bin/perl -w
> >
> >use strict;
> >use warnings;
> >use Bio::Matrix::PSM::IO;
> >
> >my $psmIO = new Bio::Matrix::PSM::IO(	-file   => 'meme.file',
> >					-format => 'meme');
> >
> >while (my $psm = $psmIO -> next_psm) {
> >   my $instances = $psm -> instances;
> >   foreach my $instance (@{ $instances }) {
> >   my $start = $instance -> start;
> >   my $score = $instance -> score;
> >   }
> >}
> >
> >********************************************************************
> >
> > 
> >

-- 
Amonida Zadissa
Biochemistry Department
Otago University
Dunedin, New Zealand
-------------- next part --------------
********************************************************************************
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= bp_example.fa
ALPHABET= ACGT
Sequence name            Weight Length  Sequence name            Weight Length  
-------------            ------ ------  -------------            ------ ------  
gi|28302128|ref|NM_00051 1.0000    626  gi|27819607|ref|NM_17391 1.0000    821  
gi|1484|emb|V00879.1|OCB 1.0000    589  gi|22873|emb|X61109.1|GG 1.0000   5881  
gi|4760585|dbj|AB020013. 1.0000    441  ref|NW_047562.1|Rn1_2084 1.0000   2212  
********************************************************************************

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

command: meme bp_example.fa -dna -mod tcm -nmotifs 5 -revcomp -minw 5 -maxw 8 

model:  mod=           tcm    nmotifs=         5    evt=           inf
object function=  E-value of product of p-values
width:  minw=            5    maxw=            8    minic=        0.00
width:  wg=             11    ws=              1    endgaps=       yes
nsites: minsites=        2    maxsites=       30    wnsites=       0.8
theta:  prob=            1    spmap=         uni    spfuzz=        0.5
em:     prior=   dirichlet    b=            0.01    maxiter=        50
        distance=    1e-05
data:   n=           10570    N=               6
strands: + -
sample: seed=            0    seqfrac=         1
Letter frequencies in dataset:
A 0.289 C 0.211 G 0.211 T 0.289 
Background letter frequencies (from dataset with add-one prior applied):
A 0.289 C 0.211 G 0.211 T 0.289 
********************************************************************************


********************************************************************************
MOTIF  1	width =    8   sites =  30   llr = 299   E-value = 4.6e-017
********************************************************************************
--------------------------------------------------------------------------------
	Motif 1 Description
--------------------------------------------------------------------------------
Simplified        A  2:4::::a
pos.-specific     C  8a:::1a:
probability       G  :::a99::
matrix            T  ::6:1:::

         bits    2.2  * *  * 
                 2.0  * *  * 
                 1.8  * * ***
                 1.6 ** *****
Information      1.3 ** *****
content          1.1 ** *****
(14.4 bits)      0.9 ********
                 0.7 ********
                 0.4 ********
                 0.2 ********
                 0.0 --------

Multilevel           CCTGGGCA
consensus              A     
sequence                     
                             
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
ref|NW_047562.1|Rn1_2084     -   1676  7.38e-06 GTGGCGAGGC CCTGGGCA GGTTGGTATC
ref|NW_047562.1|Rn1_2084     -    650  7.38e-06 TCCCACAGCT CCTGGGCA ACATGATTGT
ref|NW_047562.1|Rn1_2084     -    614  7.38e-06 TGGGCCACCA CCTGGGCA AGGAATTCTC
gi|4760585|dbj|AB020013.     +    351  7.38e-06 TGGGCCACCA CCTGGGCA AGGATTTCAC
gi|4760585|dbj|AB020013.     +    315  7.38e-06 ACTTCAGGCT CCTGGGCA ATATGATCGT
gi|4760585|dbj|AB020013.     +     81  7.38e-06 GTGGTGAGGC CCTGGGCA GGCTGCTGGT
gi|22873|emb|X61109.1|GG     +   5835  7.38e-06 TCCCACAGCT CCTGGGCA ATGTGCTGGT
gi|22873|emb|X61109.1|GG     +   4621  7.38e-06 GTGGTGAGGC CCTGGGCA GGTTGGTATC
gi|1484|emb|V00879.1|OCB     +    371  7.38e-06 ACTTCAGGCT CCTGGGCA ACGTGCTGGT
gi|1484|emb|V00879.1|OCB     +    137  7.38e-06 GTGGTGAGGC CCTGGGCA GGCTGCTGGT
gi|27819607|ref|NM_17391     +    364  7.38e-06 ACTTCAAGCT CCTGGGCA ACGTGCTAGT
gi|27819607|ref|NM_17391     +    130  7.38e-06 GTGGTGAGGC CCTGGGCA GGCTGCTGGT
gi|28302128|ref|NM_00051     +    368  7.38e-06 ACTTCAGGCT CCTGGGCA ACGTGCTGGT
gi|28302128|ref|NM_00051     +    134  7.38e-06 GTGGTGAGGC CCTGGGCA GGCTGCTGGT
ref|NW_047562.1|Rn1_2084     +    548  1.48e-05 TACTTGTGAG CCAGGGCA CTGGCCACTC
gi|4760585|dbj|AB020013.     -    417  1.48e-05 TACTTGTGAG CCAGGGCA GTGGCCACTC
gi|1484|emb|V00879.1|OCB     -    473  1.48e-05 TATTTGTGAG CCAGGGCA TTGGCCACAC
gi|27819607|ref|NM_17391     -    466  1.48e-05 TATCTGTGGG CCAGGGCA TTGGCCACAC
gi|28302128|ref|NM_00051     -    470  1.48e-05 TACTTGTGGG CCAGGGCA TTAGCCACAC
gi|22873|emb|X61109.1|GG     +   4674  2.49e-05 ACCAATAGAA ACTGGGCA TGTGGAGACA
ref|NW_047562.1|Rn1_2084     +   1219  4.51e-05 TCAACACTCC ACAGGGCA CATCCACACA
ref|NW_047562.1|Rn1_2084     +    590  4.51e-05 TGGAAGGCAG CCTGTGCA CAGGGGGAGA
gi|4760585|dbj|AB020013.     -    375  4.51e-05 TGGAAGGCAG CCTGTGCA GCGGGGGTGA
gi|22873|emb|X61109.1|GG     -   4576  4.51e-05 ACCTTGCCCC ACAGGGCA GTAACGGCAG
gi|1484|emb|V00879.1|OCB     -     92  4.51e-05 ACCTTGCCCC ACAGGGCA GTGACCGCAG
gi|28302128|ref|NM_00051     -     89  4.51e-05 ACCTTGCCCC ACAGGGCA GTAACGGCAG
gi|27819607|ref|NM_17391     -    612  5.52e-05 TTTAAATACA CCAGTGCA ATGAAAATAA
gi|28302128|ref|NM_00051     +    426  5.52e-05 ATTCACCCCA CCAGTGCA GGCTGCCTAT
gi|22873|emb|X61109.1|GG     -   4889  6.99e-05 TCCAGGTGAG CCAGGCCA TCACTAAAGG
gi|28302128|ref|NM_00051     -    272  6.99e-05 TCCAGGTGAG CCAGGCCA TCACTAAAGG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ref|NW_047562.1|Rn1_2084          4.5e-05  547_[+1]_34_[+1]_16_[-1]_28_[-1]_
                                           561_[+1]_449_[-1]_529
gi|4760585|dbj|AB020013.          4.5e-05  80_[+1]_226_[+1]_28_[+1]_16_[-1]_
                                           34_[-1]_17
gi|22873|emb|X61109.1|GG            7e-05  4575_[-1]_37_[+1]_45_[+1]_207_[-1]_
                                           938_[+1]_39
gi|1484|emb|V00879.1|OCB          4.5e-05  91_[-1]_37_[+1]_226_[+1]_94_[-1]_109
gi|27819607|ref|NM_17391          5.5e-05  129_[+1]_226_[+1]_94_[-1]_138_[-1]_
                                           202
gi|28302128|ref|NM_00051            7e-05  88_[-1]_37_[+1]_130_[-1]_88_[+1]_
                                           50_[+1]_36_[-1]_149
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 1 width=8 seqs=30
ref|NW_047562.1|Rn1_2084 ( 1676) CCTGGGCA  1 
ref|NW_047562.1|Rn1_2084 (  650) CCTGGGCA  1 
ref|NW_047562.1|Rn1_2084 (  614) CCTGGGCA  1 
gi|4760585|dbj|AB020013. (  351) CCTGGGCA  1 
gi|4760585|dbj|AB020013. (  315) CCTGGGCA  1 
gi|4760585|dbj|AB020013. (   81) CCTGGGCA  1 
gi|22873|emb|X61109.1|GG ( 5835) CCTGGGCA  1 
gi|22873|emb|X61109.1|GG ( 4621) CCTGGGCA  1 
gi|1484|emb|V00879.1|OCB (  371) CCTGGGCA  1 
gi|1484|emb|V00879.1|OCB (  137) CCTGGGCA  1 
gi|27819607|ref|NM_17391 (  364) CCTGGGCA  1 
gi|27819607|ref|NM_17391 (  130) CCTGGGCA  1 
gi|28302128|ref|NM_00051 (  368) CCTGGGCA  1 
gi|28302128|ref|NM_00051 (  134) CCTGGGCA  1 
ref|NW_047562.1|Rn1_2084 (  548) CCAGGGCA  1 
gi|4760585|dbj|AB020013. (  417) CCAGGGCA  1 
gi|1484|emb|V00879.1|OCB (  473) CCAGGGCA  1 
gi|27819607|ref|NM_17391 (  466) CCAGGGCA  1 
gi|28302128|ref|NM_00051 (  470) CCAGGGCA  1 
gi|22873|emb|X61109.1|GG ( 4674) ACTGGGCA  1 
ref|NW_047562.1|Rn1_2084 ( 1219) ACAGGGCA  1 
ref|NW_047562.1|Rn1_2084 (  590) CCTGTGCA  1 
gi|4760585|dbj|AB020013. (  375) CCTGTGCA  1 
gi|22873|emb|X61109.1|GG ( 4576) ACAGGGCA  1 
gi|1484|emb|V00879.1|OCB (   92) ACAGGGCA  1 
gi|28302128|ref|NM_00051 (   89) ACAGGGCA  1 
gi|27819607|ref|NM_17391 (  612) CCAGTGCA  1 
gi|28302128|ref|NM_00051 (  426) CCAGTGCA  1 
gi|22873|emb|X61109.1|GG ( 4889) CCAGGCCA  1 
gi|28302128|ref|NM_00051 (  272) CCAGGCCA  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 10528 bayes= 8.45094 E= 4.6e-017 
   -79    198  -1155  -1155 
 -1155    224  -1155  -1155 
    58  -1155  -1155     97 
 -1155  -1155    224  -1155 
 -1155  -1155    204   -112 
 -1155   -166    214  -1155 
 -1155    224  -1155  -1155 
   179  -1155  -1155  -1155 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 1 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 n= 10528 E= 4.6e-017 
 0.166707  0.833126  0.000070  0.000096 
 0.000096  0.999737  0.000070  0.000096 
 0.433285  0.000070  0.000070  0.566574 
 0.000096  0.000070  0.999737  0.000096 
 0.000096  0.000070  0.866448  0.133385 
 0.000096  0.066715  0.933093  0.000096 
 0.000096  0.999737  0.000070  0.000096 
 0.999763  0.000070  0.000070  0.000096 
--------------------------------------------------------------------------------





Time 82.54 secs.

********************************************************************************


********************************************************************************
MOTIF  2	width =    7   sites =  30   llr = 260   E-value = 8.7e-002
********************************************************************************
--------------------------------------------------------------------------------
	Motif 2 Description
--------------------------------------------------------------------------------
Simplified        A  8a::::7
pos.-specific     C  2:::::3
probability       G  ::aa:a:
matrix            T  ::::a::

         bits    2.2   ** * 
                 2.0   ** * 
                 1.8  ***** 
                 1.6  ***** 
Information      1.3  ***** 
content          1.1 *******
(12.5 bits)      0.9 *******
                 0.7 *******
                 0.4 *******
                 0.2 *******
                 0.0 -------

Multilevel           AAGGTGA
consensus            C     C
sequence                    
                            
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value             Site
-------------            ------  ----- ---------            -------
ref|NW_047562.1|Rn1_2084     -   1709  6.55e-05 CCTGTGGGGA AAGGTGA ACCCTGATGA
ref|NW_047562.1|Rn1_2084     -   1474  6.55e-05 GGGTAACCCT AAGGTGA AGGCCCATGG
ref|NW_047562.1|Rn1_2084     -   1453  6.55e-05 CCATGGCAAG AAGGTGA TAAACGCCTT
gi|4760585|dbj|AB020013.     +    394  6.55e-05 TGCCTTCCAG AAGGTGA TGGCTGGAGT
gi|4760585|dbj|AB020013.     +     49  6.55e-05 CCTGTGGGGA AAGGTGA ACTCCGATGA
gi|22873|emb|X61109.1|GG     +   4980  6.55e-05 TGAGAACTTC AAGGTGA GTCTATGGGA
gi|22873|emb|X61109.1|GG     +   4845  6.55e-05 GGGCAACCCT AAGGTGA AGGCTCATGG
gi|22873|emb|X61109.1|GG     +   4589  6.55e-05 CCTGTGGGGC AAGGTGA ACGTGGATGA
gi|22873|emb|X61109.1|GG     +   2336  6.55e-05 AGTCTTTAAG AAGGTGA CAATTTCTGC
gi|1484|emb|V00879.1|OCB     +    231  6.55e-05 GAACAATCCT AAGGTGA AGGCTCATGG
gi|1484|emb|V00879.1|OCB     +    105  6.55e-05 CCTGTGGGGC AAGGTGA ATGTGGAAGA
gi|27819607|ref|NM_17391     +    224  6.55e-05 GAACAACCCT AAGGTGA AGGCCCATGG
gi|27819607|ref|NM_17391     +     98  6.55e-05 CTTTTGGGGC AAGGTGA AAGTGGATGA
gi|28302128|ref|NM_00051     +    228  6.55e-05 GGGCAACCCT AAGGTGA AGGCTCATGG
gi|28302128|ref|NM_00051     +    102  6.55e-05 CCTGTGGGGC AAGGTGA ACGTGGATGA
ref|NW_047562.1|Rn1_2084     +   1401  1.13e-04 CAGATGAGCA AAGGTGC CCTTGAGGTT
gi|4760585|dbj|AB020013.     -    248  1.13e-04 GAGGCTGGCA AAGGTGC CCTTGAGGCT
gi|22873|emb|X61109.1|GG     -   4918  1.13e-04 CAGTGTGGCA AAGGTGC CCTTGAGGTT
gi|22873|emb|X61109.1|GG     -    117  1.13e-04 ATATAACAAC AAGGTGC CAAGTCTTTT
gi|1484|emb|V00879.1|OCB     -    304  1.13e-04 CAGCTTAGCA AAGGTGC CTTTGAGGTT
gi|1484|emb|V00879.1|OCB     +    252  1.13e-04 TCATGGCAAG AAGGTGC TGGCTGCCTT
gi|27819607|ref|NM_17391     -    297  1.13e-04 CAGCGCAGCA AAGGTGC CCTTGAGGTC
gi|27819607|ref|NM_17391     +    245  1.13e-04 CCATGGCAAG AAGGTGC TAGATTCCTT
gi|28302128|ref|NM_00051     -    301  1.13e-04 CAGTGTGGCA AAGGTGC CCTTGAGGTT
gi|22873|emb|X61109.1|GG     -   4898  1.61e-04 TGAGGTTGTC CAGGTGA GCCAGGCCAT
gi|22873|emb|X61109.1|GG     -   3355  1.61e-04 ATTAACTCCT CAGGTGA CGAAAAACTT
gi|22873|emb|X61109.1|GG     -     16  1.61e-04 ATGTCCCATG CAGGTGA TGTTCTCATG
gi|1484|emb|V00879.1|OCB     -    284  1.61e-04 TGAGGTTGTC CAGGTGA CTCAGACCCT
gi|28302128|ref|NM_00051     -    281  1.61e-04 TGAGGTTGTC CAGGTGA GCCAGGCCAT
ref|NW_047562.1|Rn1_2084     +   1755  1.96e-04 CAGCATCAGT CAGGTGC ACCATGGTGT
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ref|NW_047562.1|Rn1_2084           0.0002  1400_[+2]_45_[-2]_14_[-2]_228_[-2]_
                                           39_[+2]_451
gi|4760585|dbj|AB020013.          0.00011  48_[+2]_192_[-2]_139_[+2]_41
gi|22873|emb|X61109.1|GG          0.00016  15_[-2]_94_[-2]_2212_[+2]_1012_
                                           [-2]_1227_[+2]_249_[+2]_46_[-2]_
                                           13_[-2]_55_[+2]_895
gi|1484|emb|V00879.1|OCB          0.00016  104_[+2]_119_[+2]_14_[+2]_25_[-2]_
                                           13_[-2]_279
gi|27819607|ref|NM_17391          0.00011  97_[+2]_119_[+2]_14_[+2]_45_[-2]_518
gi|28302128|ref|NM_00051          0.00016  101_[+2]_119_[+2]_46_[-2]_13_[-2]_319
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 2 width=7 seqs=30
ref|NW_047562.1|Rn1_2084 ( 1709) AAGGTGA  1 
ref|NW_047562.1|Rn1_2084 ( 1474) AAGGTGA  1 
ref|NW_047562.1|Rn1_2084 ( 1453) AAGGTGA  1 
gi|4760585|dbj|AB020013. (  394) AAGGTGA  1 
gi|4760585|dbj|AB020013. (   49) AAGGTGA  1 
gi|22873|emb|X61109.1|GG ( 4980) AAGGTGA  1 
gi|22873|emb|X61109.1|GG ( 4845) AAGGTGA  1 
gi|22873|emb|X61109.1|GG ( 4589) AAGGTGA  1 
gi|22873|emb|X61109.1|GG ( 2336) AAGGTGA  1 
gi|1484|emb|V00879.1|OCB (  231) AAGGTGA  1 
gi|1484|emb|V00879.1|OCB (  105) AAGGTGA  1 
gi|27819607|ref|NM_17391 (  224) AAGGTGA  1 
gi|27819607|ref|NM_17391 (   98) AAGGTGA  1 
gi|28302128|ref|NM_00051 (  228) AAGGTGA  1 
gi|28302128|ref|NM_00051 (  102) AAGGTGA  1 
ref|NW_047562.1|Rn1_2084 ( 1401) AAGGTGC  1 
gi|4760585|dbj|AB020013. (  248) AAGGTGC  1 
gi|22873|emb|X61109.1|GG ( 4918) AAGGTGC  1 
gi|22873|emb|X61109.1|GG (  117) AAGGTGC  1 
gi|1484|emb|V00879.1|OCB (  304) AAGGTGC  1 
gi|1484|emb|V00879.1|OCB (  252) AAGGTGC  1 
gi|27819607|ref|NM_17391 (  297) AAGGTGC  1 
gi|27819607|ref|NM_17391 (  245) AAGGTGC  1 
gi|28302128|ref|NM_00051 (  301) AAGGTGC  1 
gi|22873|emb|X61109.1|GG ( 4898) CAGGTGA  1 
gi|22873|emb|X61109.1|GG ( 3355) CAGGTGA  1 
gi|22873|emb|X61109.1|GG (   16) CAGGTGA  1 
gi|1484|emb|V00879.1|OCB (  284) CAGGTGA  1 
gi|28302128|ref|NM_00051 (  281) CAGGTGA  1 
ref|NW_047562.1|Rn1_2084 ( 1755) CAGGTGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 7 n= 10534 bayes= 9.12753 E= 8.7e-002 
   147     -8  -1155  -1155 
   179  -1155  -1155  -1155 
 -1155  -1155    224  -1155 
 -1155  -1155    224  -1155 
 -1155  -1155  -1155    179 
 -1155  -1155    224  -1155 
   121     66  -1155  -1155 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 2 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 7 n= 10534 E= 8.7e-002 
 0.799830  0.200004  0.000070  0.000096 
 0.999763  0.000070  0.000070  0.000096 
 0.000096  0.000070  0.999737  0.000096 
 0.000096  0.000070  0.999737  0.000096 
 0.000096  0.000070  0.000070  0.999763 
 0.000096  0.000070  0.999737  0.000096 
 0.666541  0.333293  0.000070  0.000096 
--------------------------------------------------------------------------------





Time 162.14 secs.

********************************************************************************


********************************************************************************
MOTIF  3	width =    8   sites =  25   llr = 239   E-value = 6.8e-005
********************************************************************************
--------------------------------------------------------------------------------
	Motif 3 Description
--------------------------------------------------------------------------------
Simplified        A  ::6:::::
pos.-specific     C  ::4:4a::
probability       G  7a::6::a
matrix            T  3::a::a:

         bits    2.2  *   * *
                 2.0  *   * *
                 1.8  * * ***
                 1.6  * * ***
Information      1.3  * *****
content          1.1 ** *****
(13.8 bits)      0.9 ********
                 0.7 ********
                 0.4 ********
                 0.2 ********
                 0.0 --------

Multilevel           GGATGCTG
consensus            T C C   
sequence                     
                             
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
ref|NW_047562.1|Rn1_2084     -   1733  7.38e-06 ATGCTGAGAA GGCTGCTG TTAATGGCCT
ref|NW_047562.1|Rn1_2084     -   1559  7.38e-06 TCCCTTTGTA GGCTGCTG GTTGTCTACC
gi|4760585|dbj|AB020013.     +     89  7.38e-06 GCCCTGGGCA GGCTGCTG GTTGTCTACC
gi|4760585|dbj|AB020013.     +     24  7.38e-06 ATGCTGAGAA GGCTGCTG TCTCTGGCCT
gi|22873|emb|X61109.1|GG     +   4759  7.38e-06 CCCACCCTTA GGCTGCTG GTGGTCTACC
gi|1484|emb|V00879.1|OCB     +    145  7.38e-06 GCCCTGGGCA GGCTGCTG GTTGTCTACC
gi|27819607|ref|NM_17391     +    138  7.38e-06 GCCCTGGGCA GGCTGCTG GTTGTCTACC
gi|28302128|ref|NM_00051     +    142  7.38e-06 GCCCTGGGCA GGCTGCTG GTGGTCTACC
ref|NW_047562.1|Rn1_2084     +   1956  1.75e-05 ATCTCTCCCT GGATGCTG GGCCACTGGC
ref|NW_047562.1|Rn1_2084     +   1859  2.49e-05 TGCTCTGCCT GGCTCCTG CTCTCGCTGT
gi|22873|emb|X61109.1|GG     -   4439  2.49e-05 GCCCAGCCCT GGCTCCTG CCCTCCCTGC
ref|NW_047562.1|Rn1_2084     -   1354  3.50e-05 AGCTGCATGT GGATCCTG AGAACTTCAG
gi|4760585|dbj|AB020013.     +    294  3.50e-05 AGCTCCATGT GGATCCTG AGAACTTCAG
gi|22873|emb|X61109.1|GG     +   4964  3.50e-05 AGCTGCACGT GGATCCTG AGAACTTCAA
gi|1484|emb|V00879.1|OCB     +    350  3.50e-05 AGCTGCACGT GGATCCTG AGAACTTCAG
gi|27819607|ref|NM_17391     +    343  3.50e-05 AGCTGCATGT GGATCCTG AGAACTTCAA
gi|28302128|ref|NM_00051     +    347  3.50e-05 AGCTGCACGT GGATCCTG AGAACTTCAG
ref|NW_047562.1|Rn1_2084     -   1917  5.89e-05 CACCGAAGCC TGATGCTG TAGAGCCACA
ref|NW_047562.1|Rn1_2084     -   1745  5.89e-05 TGCACCTGAC TGATGCTG AGAAGGCTGC
gi|4760585|dbj|AB020013.     +     12  5.89e-05 TGCACCTGAC TGATGCTG AGAAGGCTGC
gi|22873|emb|X61109.1|GG     +   4823  5.89e-05 TGTCCACTCC TGATGCTG TTATGGGCAA
gi|27819607|ref|NM_17391     +    202  5.89e-05 TGTCCACTGC TGATGCTG TTATGAACAA
gi|28302128|ref|NM_00051     +    206  5.89e-05 TGTCCACTCC TGATGCTG TTATGGGCAA
gi|22873|emb|X61109.1|GG     -   4424  6.90e-05 CTGCCCTCCC TGCTCCTG GGAGTAGATT
gi|22873|emb|X61109.1|GG     -   5118  8.28e-05 GAAACTAAAA TGATCCTG AGAGTTCCAC
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ref|NW_047562.1|Rn1_2084          5.9e-05  1353_[-3]_197_[-3]_166_[-3]_4_[-3]_
                                           106_[+3]_50_[-3]_31_[+3]_249
gi|4760585|dbj|AB020013.          5.9e-05  11_[+3]_4_[+3]_57_[+3]_197_[+3]_140
gi|22873|emb|X61109.1|GG          8.3e-05  4423_[-3]_7_[-3]_312_[+3]_56_[+3]_
                                           133_[+3]_146_[-3]_756
gi|1484|emb|V00879.1|OCB          3.5e-05  144_[+3]_197_[+3]_232
gi|27819607|ref|NM_17391          5.9e-05  137_[+3]_56_[+3]_133_[+3]_471
gi|28302128|ref|NM_00051          5.9e-05  141_[+3]_56_[+3]_133_[+3]_272
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 3 width=8 seqs=25
ref|NW_047562.1|Rn1_2084 ( 1733) GGCTGCTG  1 
ref|NW_047562.1|Rn1_2084 ( 1559) GGCTGCTG  1 
gi|4760585|dbj|AB020013. (   89) GGCTGCTG  1 
gi|4760585|dbj|AB020013. (   24) GGCTGCTG  1 
gi|22873|emb|X61109.1|GG ( 4759) GGCTGCTG  1 
gi|1484|emb|V00879.1|OCB (  145) GGCTGCTG  1 
gi|27819607|ref|NM_17391 (  138) GGCTGCTG  1 
gi|28302128|ref|NM_00051 (  142) GGCTGCTG  1 
ref|NW_047562.1|Rn1_2084 ( 1956) GGATGCTG  1 
ref|NW_047562.1|Rn1_2084 ( 1859) GGCTCCTG  1 
gi|22873|emb|X61109.1|GG ( 4439) GGCTCCTG  1 
ref|NW_047562.1|Rn1_2084 ( 1354) GGATCCTG  1 
gi|4760585|dbj|AB020013. (  294) GGATCCTG  1 
gi|22873|emb|X61109.1|GG ( 4964) GGATCCTG  1 
gi|1484|emb|V00879.1|OCB (  350) GGATCCTG  1 
gi|27819607|ref|NM_17391 (  343) GGATCCTG  1 
gi|28302128|ref|NM_00051 (  347) GGATCCTG  1 
ref|NW_047562.1|Rn1_2084 ( 1917) TGATGCTG  1 
ref|NW_047562.1|Rn1_2084 ( 1745) TGATGCTG  1 
gi|4760585|dbj|AB020013. (   12) TGATGCTG  1 
gi|22873|emb|X61109.1|GG ( 4823) TGATGCTG  1 
gi|27819607|ref|NM_17391 (  202) TGATGCTG  1 
gi|28302128|ref|NM_00051 (  206) TGATGCTG  1 
gi|22873|emb|X61109.1|GG ( 4424) TGCTCCTG  1 
gi|22873|emb|X61109.1|GG ( 5118) TGATCCTG  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 10528 bayes= 8.49998 E= 6.8e-005 
 -1129  -1129    169     15 
 -1129  -1129    224  -1129 
    95    106  -1129  -1129 
 -1129  -1129  -1129    179 
 -1129     92    151  -1129 
 -1129    224  -1129  -1129 
 -1129  -1129  -1129    179 
 -1129  -1129    224  -1129 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 3 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 n= 10528 E= 6.8e-005 
 0.000116  0.000084  0.679812  0.319988 
 0.000116  0.000084  0.999685  0.000116 
 0.559892  0.439908  0.000084  0.000116 
 0.000116  0.000084  0.000084  0.999716 
 0.000116  0.399924  0.599844  0.000116 
 0.000116  0.999685  0.000084  0.000116 
 0.000116  0.000084  0.000084  0.999716 
 0.000116  0.000084  0.999685  0.000116 
--------------------------------------------------------------------------------





Time 239.91 secs.

********************************************************************************


********************************************************************************
MOTIF  4	width =    8   sites =  18   llr = 177   E-value = 1.9e+000
********************************************************************************
--------------------------------------------------------------------------------
	Motif 4 Description
--------------------------------------------------------------------------------
Simplified        A  ::3:5:::
pos.-specific     C  :3:::::a
probability       G  a7:a:aa:
matrix            T  ::7:5:::

         bits    2.2 *  * ***
                 2.0 *  * ***
                 1.8 *  * ***
                 1.6 *  * ***
Information      1.3 ** * ***
content          1.1 ** * ***
(14.2 bits)      0.9 ********
                 0.7 ********
                 0.4 ********
                 0.2 ********
                 0.0 --------

Multilevel           GGTGAGGC
consensus             CA T   
sequence                     
                             
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
ref|NW_047562.1|Rn1_2084     +   1905  1.48e-05 CCAATACCAG GGTGTGGC TCTACAGCAT
gi|4760585|dbj|AB020013.     +     73  1.48e-05 TGAAGTTGGT GGTGAGGC CCTGGGCAGG
gi|22873|emb|X61109.1|GG     +   4613  1.48e-05 TGAAGTTGGT GGTGAGGC CCTGGGCAGG
gi|22873|emb|X61109.1|GG     -   4394  1.48e-05 CCAACCCTAG GGTGTGGC TCCACAGGGT
gi|1484|emb|V00879.1|OCB     +    462  1.48e-05 GGTGGTGGCT GGTGTGGC CAATGCCCTG
gi|1484|emb|V00879.1|OCB     +    129  1.48e-05 AGAAGTTGGT GGTGAGGC CCTGGGCAGG
gi|27819607|ref|NM_17391     +    455  1.48e-05 GGTGGTGGCT GGTGTGGC CAATGCCCTG
gi|27819607|ref|NM_17391     +    122  1.48e-05 TGAAGTTGGT GGTGAGGC CCTGGGCAGG
gi|28302128|ref|NM_00051     +    459  1.48e-05 AGTGGTGGCT GGTGTGGC TAATGCCCTG
gi|28302128|ref|NM_00051     +    126  1.48e-05 TGAAGTTGGT GGTGAGGC CCTGGGCAGG
ref|NW_047562.1|Rn1_2084     -    559  4.43e-05 GGTGGTGGCT GGAGTGGC CAGTGCCCTG
gi|4760585|dbj|AB020013.     +    406  4.43e-05 GGTGATGGCT GGAGTGGC CACTGCCCTG
gi|22873|emb|X61109.1|GG     +   1897  4.43e-05 ACCTGCACCT GCTGTGGC ATCCATTCAC
gi|22873|emb|X61109.1|GG     +    951  4.43e-05 TACGCGGGAG GCTGAGGC AGGAGAATGG
ref|NW_047562.1|Rn1_2084     +   1497  5.90e-05 ACCCATGATA GCAGAGGC AGAGGACAGG
gi|4760585|dbj|AB020013.     -    151  5.90e-05 ACCCATGATA GCAGAGGC AGAGGATAGG
gi|22873|emb|X61109.1|GG     -   1009  5.90e-05 AGGCTGGAGT GCAGTGGC GCGATCTCGG
gi|27819607|ref|NM_17391     -    581  5.90e-05 TCTTTATTAG GCAGAGGC CAGATGCTCA
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
ref|NW_047562.1|Rn1_2084          5.9e-05  558_[-4]_930_[+4]_400_[+4]_300
gi|4760585|dbj|AB020013.          5.9e-05  72_[+4]_70_[-4]_247_[+4]_28
gi|22873|emb|X61109.1|GG          5.9e-05  950_[+4]_50_[-4]_880_[+4]_2489_
                                           [-4]_211_[+4]_1261
gi|1484|emb|V00879.1|OCB          1.5e-05  128_[+4]_325_[+4]_120
gi|27819607|ref|NM_17391          5.9e-05  121_[+4]_325_[+4]_118_[-4]_233
gi|28302128|ref|NM_00051          1.5e-05  125_[+4]_325_[+4]_160
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 4 width=8 seqs=18
ref|NW_047562.1|Rn1_2084 ( 1905) GGTGTGGC  1 
gi|4760585|dbj|AB020013. (   73) GGTGAGGC  1 
gi|22873|emb|X61109.1|GG ( 4613) GGTGAGGC  1 
gi|22873|emb|X61109.1|GG ( 4394) GGTGTGGC  1 
gi|1484|emb|V00879.1|OCB (  462) GGTGTGGC  1 
gi|1484|emb|V00879.1|OCB (  129) GGTGAGGC  1 
gi|27819607|ref|NM_17391 (  455) GGTGTGGC  1 
gi|27819607|ref|NM_17391 (  122) GGTGAGGC  1 
gi|28302128|ref|NM_00051 (  459) GGTGTGGC  1 
gi|28302128|ref|NM_00051 (  126) GGTGAGGC  1 
ref|NW_047562.1|Rn1_2084 (  559) GGAGTGGC  1 
gi|4760585|dbj|AB020013. (  406) GGAGTGGC  1 
gi|22873|emb|X61109.1|GG ( 1897) GCTGTGGC  1 
gi|22873|emb|X61109.1|GG (  951) GCTGAGGC  1 
ref|NW_047562.1|Rn1_2084 ( 1497) GCAGAGGC  1 
gi|4760585|dbj|AB020013. (  151) GCAGAGGC  1 
gi|22873|emb|X61109.1|GG ( 1009) GCAGTGGC  1 
gi|27819607|ref|NM_17391 (  581) GCAGAGGC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 10528 bayes= 10.5955 E= 1.9e+000 
 -1081  -1081    224  -1081 
 -1081     66    166  -1081 
    21  -1081  -1081    121 
 -1081  -1081    224  -1081 
    79  -1081  -1081     79 
 -1081  -1081    224  -1081 
 -1081  -1081    224  -1081 
 -1081    224  -1081  -1081 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 4 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 n= 10528 E= 1.9e+000 
 0.000160  0.000117  0.999562  0.000160 
 0.000160  0.333265  0.666414  0.000160 
 0.333309  0.000117  0.000117  0.666457 
 0.000160  0.000117  0.999562  0.000160 
 0.499883  0.000117  0.000117  0.499883 
 0.000160  0.000117  0.999562  0.000160 
 0.000160  0.000117  0.999562  0.000160 
 0.000160  0.999562  0.000117  0.000160 
--------------------------------------------------------------------------------





Time 316.66 secs.

********************************************************************************


********************************************************************************
MOTIF  5	width =    8   sites =  15   llr = 151   E-value = 4.3e+001
********************************************************************************
--------------------------------------------------------------------------------
	Motif 5 Description
--------------------------------------------------------------------------------
Simplified        A  a:a:a:a:
pos.-specific     C  :a:7:8:a
probability       G  :::3:2::
matrix            T  ::::::::

         bits    2.2  *     *
                 2.0  *     *
                 1.8 *** * **
                 1.6 *** ****
Information      1.3 ********
content          1.1 ********
(14.5 bits)      0.9 ********
                 0.7 ********
                 0.4 ********
                 0.2 ********
                 0.0 --------

Multilevel           ACACACAC
consensus               G G  
sequence                     
                             
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 sites sorted by position p-value
--------------------------------------------------------------------------------
Sequence name            Strand  Start   P-value              Site
-------------            ------  ----- ---------            --------
gi|22873|emb|X61109.1|GG     -   1841  1.38e-05 ACCACAACAC ACACACAC ACACACACAC
gi|22873|emb|X61109.1|GG     -   1833  1.38e-05 ACACACACAC ACACACAC ACACACACAC
gi|22873|emb|X61109.1|GG     -   1825  1.38e-05 ACACACACAC ACACACAC ACACACACAC
gi|22873|emb|X61109.1|GG     -   1817  1.38e-05 ACACACACAC ACACACAC ACACACACAC
gi|22873|emb|X61109.1|GG     -   1809  1.38e-05 ACACACACAC ACACACAC ACACACACAC
gi|22873|emb|X61109.1|GG     -   1799  1.38e-05 ACACACACAC ACACACAC AAGTCCTCAA
gi|22873|emb|X61109.1|GG     -    533  1.38e-05 TTTCACACAC ACACACAC CCTTTCATTC
ref|NW_047562.1|Rn1_2084     -   1768  2.77e-05 AAACTCAGAA ACAGACAC CATGGTGCAC
gi|22873|emb|X61109.1|GG     +   4529  2.77e-05 GCAACCTCAA ACAGACAC CATGGTGCAC
gi|22873|emb|X61109.1|GG     +    222  2.77e-05 GAATAGATCA ACAGACAC CCAGGCCTAC
gi|27819607|ref|NM_17391     +     44  2.77e-05 AACTACACAA ACAGACAC CATGCTGACT
gi|28302128|ref|NM_00051     +     42  2.77e-05 GCAACCTCAA ACAGACAC CATGGTGCAT
gi|22873|emb|X61109.1|GG     -   5851  4.15e-05 ATGGGCCAGC ACACAGAC CAGCACATTG
gi|22873|emb|X61109.1|GG     -   1273  4.15e-05 AATAAAGTCA ACACAGAC AGAACTTTGC
gi|28302128|ref|NM_00051     -    384  4.15e-05 ATGGGCCAGC ACACAGAC CAGCACGTTG
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 block diagrams
--------------------------------------------------------------------------------
SEQUENCE NAME            POSITION P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
gi|22873|emb|X61109.1|GG          4.1e-05  221_[+5]_303_[-5]_732_[-5]_518_
                                           [-5]_2_[-5]_[-5]_[-5]_[-5]_[-5]_
                                           2680_[+5]_1314_[-5]_23
ref|NW_047562.1|Rn1_2084          2.8e-05  1767_[-5]_437
gi|27819607|ref|NM_17391          2.8e-05  43_[+5]_770
gi|28302128|ref|NM_00051          4.1e-05  41_[+5]_334_[-5]_235
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 in BLOCKS format
--------------------------------------------------------------------------------
BL   MOTIF 5 width=8 seqs=15
gi|22873|emb|X61109.1|GG ( 1841) ACACACAC  1 
gi|22873|emb|X61109.1|GG ( 1833) ACACACAC  1 
gi|22873|emb|X61109.1|GG ( 1825) ACACACAC  1 
gi|22873|emb|X61109.1|GG ( 1817) ACACACAC  1 
gi|22873|emb|X61109.1|GG ( 1809) ACACACAC  1 
gi|22873|emb|X61109.1|GG ( 1799) ACACACAC  1 
gi|22873|emb|X61109.1|GG (  533) ACACACAC  1 
ref|NW_047562.1|Rn1_2084 ( 1768) ACAGACAC  1 
gi|22873|emb|X61109.1|GG ( 4529) ACAGACAC  1 
gi|22873|emb|X61109.1|GG (  222) ACAGACAC  1 
gi|27819607|ref|NM_17391 (   44) ACAGACAC  1 
gi|28302128|ref|NM_00051 (   42) ACAGACAC  1 
gi|22873|emb|X61109.1|GG ( 5851) ACACAGAC  1 
gi|22873|emb|X61109.1|GG ( 1273) ACACAGAC  1 
gi|28302128|ref|NM_00051 (  384) ACACAGAC  1 
//

--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific scoring matrix
--------------------------------------------------------------------------------
log-odds matrix: alength= 4 w= 8 n= 10528 bayes= 9.37792 E= 4.3e+001 
   179  -1055  -1055  -1055 
 -1055    224  -1055  -1055 
   179  -1055  -1055  -1055 
 -1055    166     66  -1055 
   179  -1055  -1055  -1055 
 -1055    192     -8  -1055 
   179  -1055  -1055  -1055 
 -1055    224  -1055  -1055 
--------------------------------------------------------------------------------

--------------------------------------------------------------------------------
	Motif 5 position-specific probability matrix
--------------------------------------------------------------------------------
letter-probability matrix: alength= 4 w= 8 n= 10528 E= 4.3e+001 
 0.999526  0.000141  0.000141  0.000193 
 0.000193  0.999474  0.000141  0.000193 
 0.999526  0.000141  0.000141  0.000193 
 0.000193  0.666363  0.333252  0.000193 
 0.999526  0.000141  0.000141  0.000193 
 0.000193  0.799608  0.200007  0.000193 
 0.999526  0.000141  0.000141  0.000193 
 0.000193  0.999474  0.000141  0.000193 
--------------------------------------------------------------------------------





Time 392.22 secs.

********************************************************************************


********************************************************************************
SUMMARY OF MOTIFS
********************************************************************************

--------------------------------------------------------------------------------
	Combined block diagrams: non-overlapping sites with p-value < 0.0001
--------------------------------------------------------------------------------
SEQUENCE NAME            COMBINED P-VALUE  MOTIF DIAGRAM
-------------            ----------------  -------------
gi|28302128|ref|NM_00051         2.85e-05  41_[+5(2.77e-05)]_39_[-1(4.51e-05)]_5_[+2(6.55e-05)]_17_[+4(1.48e-05)]_[+1(7.38e-06)]_[+3(7.38e-06)]_56_[+3(5.89e-05)]_14_[+2(6.55e-05)]_37_[-1(6.99e-05)]_45_[-1(9.76e-05)]_14_[+3(3.50e-05)]_13_[+1(7.38e-06)]_8_[-5(4.15e-05)]_34_[+1(5.52e-05)]_25_[+4(1.48e-05)]_3_[-1(1.48e-05)]_149
gi|27819607|ref|NM_17391         8.35e-05  43_[+5(2.77e-05)]_46_[+2(6.55e-05)]_17_[+4(1.48e-05)]_[+1(7.38e-06)]_[+3(7.38e-06)]_56_[+3(5.89e-05)]_14_[+2(6.55e-05)]_90_[-1(9.76e-05)]_14_[+3(3.50e-05)]_13_[+1(7.38e-06)]_83_[+4(1.48e-05)]_3_[-1(1.48e-05)]_107_[-4(5.90e-05)]_23_[-1(5.52e-05)]_202
gi|1484|emb|V00879.1|OCB         2.09e-04  91_[-1(4.51e-05)]_5_[+2(6.55e-05)]_17_[+4(1.48e-05)]_[+1(7.38e-06)]_[+3(7.38e-06)]_78_[+2(6.55e-05)]_90_[-1(9.76e-05)]_14_[+3(3.50e-05)]_13_[+1(7.38e-06)]_83_[+4(1.48e-05)]_3_[-1(1.48e-05)]_109
gi|22873|emb|X61109.1|GG         4.47e-02  221_[+5(2.77e-05)]_303_[-5(1.38e-05)]_410_[+4(4.43e-05)]_50_[-4(5.90e-05)]_256_[-5(4.15e-05)]_518_[-5(1.38e-05)]_[-5(1.38e-05)]_[-5(1.38e-05)]_[-5(1.38e-05)]_[-5(1.38e-05)]_[-5(1.38e-05)]_50_[+4(4.43e-05)]_431_[+2(6.55e-05)]_2051_[-4(1.48e-05)]_22_[-3(6.90e-05)]_7_[-3(2.49e-05)]_82_[+5(2.77e-05)]_39_[-1(4.51e-05)]_5_[+2(6.55e-05)]_17_[+4(1.48e-05)]_[+1(7.38e-06)]_45_[+1(2.49e-05)]_77_[+3(7.38e-06)]_56_[+3(5.89e-05)]_14_[+2(6.55e-05)]_37_[-1(6.99e-05)]_45_[-1(9.76e-05)]_14_[+3(3.50e-05)]_8_[+2(6.55e-05)]_131_[-3(8.28e-05)]_709_[+1(7.38e-06)]_8_[-5(4.15e-05)]_23
gi|4760585|dbj|AB020013.         9.31e-05  11_[+3(5.89e-05)]_4_[+3(7.38e-06)]_17_[+2(6.55e-05)]_17_[+4(1.48e-05)]_[+1(7.38e-06)]_[+3(7.38e-06)]_54_[-4(5.90e-05)]_135_[+3(3.50e-05)]_13_[+1(7.38e-06)]_28_[+1(7.38e-06)]_16_[-1(4.51e-05)]_11_[+2(6.55e-05)]_5_[+4(4.43e-05)]_3_[-1(1.48e-05)]_17
ref|NW_047562.1|Rn1_2084         3.25e-03  547_[+1(1.48e-05)]_3_[-4(4.43e-05)]_23_[+1(4.51e-05)]_16_[-1(7.38e-06)]_28_[-1(7.38e-06)]_561_[+1(4.51e-05)]_127_[-3(3.50e-05)]_91_[-2(6.55e-05)]_14_[-2(6.55e-05)]_16_[+4(5.90e-05)]_54_[-3(7.38e-06)]_109_[-1(7.38e-06)]_[-4(9.13e-05)]_17_[-2(6.55e-05)]_17_[-3(7.38e-06)]_4_[-3(5.89e-05)]_15_[-5(2.77e-05)]_60_[-4(6.98e-05)]_15_[+3(2.49e-05)]_38_[+4(1.48e-05)]_4_[-3(5.89e-05)]_31_[+3(1.75e-05)]_249
--------------------------------------------------------------------------------

********************************************************************************


********************************************************************************
Stopped because nmotifs = 5 reached.
********************************************************************************

CPU: veggie

********************************************************************************


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