DanRer7 conservation lastz parameters: Difference between revisions

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(only need HoxD55 matrix)
(fixup M=40M mistake)
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<TR><TH>query</TH>
<TR><TH>query</TH>
   <TH>abridged<BR>repeats(no)</TH>
   <TH>abridged<BR>repeats(no)</TH>
   <TH>M(40M)</TH><TH>K(3000)</TH>
   <TH>M(0)</TH><TH>K(3000)</TH>
   <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
   <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
   <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH>
   <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH>
Line 65: Line 65:
<TR>
<TR>
   <TH>X. tropicalis&nbsp;xenTro2</TH>
   <TH>X. tropicalis&nbsp;xenTro2</TH>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <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>
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<TR>
<TR>
   <TH>Mouse&nbsp;mm9</TH>
   <TH>Mouse&nbsp;mm9</TH>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <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>5.104%</TD>
   <TD>2010-12-17</TD><TD ALIGN=RIGHT>5.104%</TD>
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<TR>
<TR>
   <TH>Human&nbsp;hg19</TH>
   <TH>Human&nbsp;hg19</TH>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <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>2010-12-20</TD><TD ALIGN=RIGHT>6.151%</TD>
   <TD>2010-12-20</TD><TD ALIGN=RIGHT>6.151%</TD>

Revision as of 19:57, 4 February 2011

See Also:

The HoxD55
scoring matrix is:
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

do not edit, automatically generated table

query abridged
repeats(no)		 M(0)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 no022006000HoxD55.q 3400lastz3020004001 2010-12-176.428% 6.610%
Mouse mm9 no022006000HoxD55.q 3400lastz3020004001 2010-12-175.104% 2.602%
Human hg19 no022006000HoxD55.q 3400lastz3020004001 2010-12-206.151% 2.790%
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