DanRer7 conservation lastz parameters: Difference between revisions

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==See Also:==
==see also==


<UL>
<UL>
<LI>[[DanRer7 Genome size statistics]]</LI>
<LI>Zebrafish 8-way [[DanRer7 Genome size statistics]]</LI>
<LI>[[DanRer7 conservation alignment]]</LI>
<LI>Zebrafish 8-way [[DanRer7 conservation alignment]]</LI>
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 Andy's alignment notes]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
</UL>
</UL>


<TABLE BORDER=0>
<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<TR><TD>The HoxD55<BR>scoring matrix is:</TD></TR>
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The human-chimp.v2<BR>scoring matrix is:</TD></TR>


<TR><TD>
<TR><TD><TABLE BORDER=1>
<TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>
<TR><TH>C</TH><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>
<TR><TH>G</TH><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>
<TR><TH>T</TH><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
<TR><TH>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
Line 33: Line 19:
</TABLE>
</TABLE>
O=400 E=30
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>90</TD><TD>-330</TD><TD>-236</TD><TD>-356</TD></TR>
<TR><TH>C</TH><TD>-330</TD><TD>100</TD><TD>-318</TD><TD>-236</TD></TR>
<TR><TH>G</TH><TD>-236</TD><TD>-318</TD><TD>100</TD><TD>-330</TD></TR>
<TR><TH>T</TH><TD>-356</TD><TD>-236</TD><TD>-330</TD><TD>90</TD></TR>
</TABLE>
O=600 E=150
</TD>
</TD>
</TR></TABLE>
</TR></TABLE>
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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>
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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>
   <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>
   <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>0</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>0</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>

Latest revision as of 20:20, 19 May 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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