DanRer7 conservation lastz parameters: Difference between revisions

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(updated for hg19 and mm9)
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   <TH>chain&nbsp;table<BR>date</TH>
   <TH>chain&nbsp;table<BR>date</TH>
   <TH>%&nbsp;of&nbsp;danRer7<BR>matched<BR>(chainLink&nbsp;table)</TH>
   <TH>%&nbsp;of&nbsp;danRer7<BR>matched<BR>(chainLink&nbsp;table)</TH>
   <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkCe9)</TH>
   <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkDanRer7)</TH>
</TR>
</TR>
<TR>
<TR>
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   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>10.270%</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>10.270%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>27.522%</TD></TR>
<TR>
<TR>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TH>Medaka&nbsp;oryLat2</TH>
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   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>10.032%</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>10.032%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>17.780%</TD></TR>
<TR>
<TR>
   <TH>Tetraodon&nbsp;tetNig2</TH>
   <TH>Tetraodon&nbsp;tetNig2</TH>
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   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>6.273%</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>6.273%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>23.571%</TD></TR>
<TR>
<TR>
   <TH>Fugu&nbsp;fr2</TH>
   <TH>Fugu&nbsp;fr2</TH>
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   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2010-12-21</TD><TD ALIGN=RIGHT>7.363%</TD>
   <TD>2010-12-21</TD><TD ALIGN=RIGHT>7.363%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>20.360%</TD></TR>
<TR>
<TR>
   <TH>X. tropicalis&nbsp;xenTro2</TH>
   <TH>X. tropicalis&nbsp;xenTro2</TH>
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   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>6.428%</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>6.428%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>6.610%</TD></TR>
<TR>
<TR>
   <TH>Mouse&nbsp;mm9</TH>
   <TH>Mouse&nbsp;mm9</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
</TR><TR>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2010-12-17</TD><TD ALIGN=RIGHT>5.104%</TD>
  <TD ALIGN=RIGHT>2.602%</TD></TR>
<TR>
   <TH>Human&nbsp;hg19</TH>
   <TH>Human&nbsp;hg19</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
</TR>
  <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2010-12-20</TD><TD ALIGN=RIGHT>6.151%</TD>
  <TD ALIGN=RIGHT>2.790%</TD></TR>
 
</TABLE>
</TABLE>

Revision as of 19:46, 4 February 2011

See Also:

The default
scoring matrix is:		  The HoxD55
scoring matrix is:		 The human-chimp.v2
scoring matrix is:
 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

O=400 E=30

 
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

 
 ACGT
A90-330-236-356
C-330100-318-236
G-236-318100-330
T-356-236-33090

O=600 E=150

do not edit, automatically generated table

query abridged
repeats(no)		 M(40M)K(3000) L(3000)QY(9400) program
run		E(30)H(0) O(400)T(1) chain table
date		 % of danRer7
matched
(chainLink table)		 % of query
matched
(chainLinkDanRer7)
Stickleback gasAcu1 no5030003000HoxD55.q 9400lastz3004001 2010-12-1710.270% 27.522%
Medaka oryLat2 no5030003000HoxD55.q 9400lastz3004001 2010-12-1710.032% 17.780%
Tetraodon tetNig2 no5030003000HoxD55.q 9400lastz3004001 2010-12-176.273% 23.571%
Fugu fr2 no5030003000HoxD55.q 9400lastz3004001 2010-12-217.363% 20.360%
X. tropicalis xenTro2 no40M22006000HoxD55.q 3400lastz3020004001 2010-12-176.428% 6.610%
Mouse mm9 no40M22006000HoxD55.q 3400lastz3020004001 2010-12-175.104% 2.602%
Human hg19 no40M22006000HoxD55.q 3400lastz3020004001 2010-12-206.151% 2.790%
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