View source for Fr3 conservation lastz parameters

==See Also==

<UL>
<LI>Fugu 8-way [[Fr3 Genome size statistics]]</LI>
<LI>Fugu 8-way [[Fr3 conservation alignment]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>


<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<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>
<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>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
<TR><TH>C</TH><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>
<TR><TH>G</TH><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>
<TR><TH>T</TH><TD>-100</TD><TD>-25</TD><TD>-90</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>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>
</TR></TABLE>

==do not edit, automatically generated table==
<TABLE BORDER=1>
<TR><TH>query</TH>
  <TH>abridged<BR>repeats(no)</TH>
  <TH>M(0)</TH><TH>K(3000)</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>O(400)</TH><TH>T(1)</TH>
  <TH>chain&nbsp;table<BR>date</TH>
  <TH>%&nbsp;of&nbsp;fr3<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkFr3)</TH>
</TR>
<TR>
  <TH>Tetraodon&nbsp;tetNig2</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2011-12-01</TD><TD ALIGN=RIGHT>70.912%</TD>
  <TD ALIGN=RIGHT>80.674%</TD></TR>
<TR>
  <TH>Nile tilapia&nbsp;oreNil1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2011-12-02</TD><TD ALIGN=RIGHT>57.240%</TD>
  <TD ALIGN=RIGHT>30.736%</TD></TR>
<TR>
  <TH>Stickleback&nbsp;gasAcu1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2011-12-02</TD><TD ALIGN=RIGHT>55.527%</TD>
  <TD ALIGN=RIGHT>48.038%</TD></TR>
<TR>
  <TH>Atlantic cod&nbsp;gadMor1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2012-01-14</TD><TD ALIGN=RIGHT>30.327%</TD>
  <TD ALIGN=RIGHT>19.051%</TD></TR>
<TR>
  <TH>Medaka&nbsp;oryLat2</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2011-12-02</TD><TD ALIGN=RIGHT>43.863%</TD>
  <TD ALIGN=RIGHT>25.905%</TD></TR>
<TR>
  <TH>Zebrafish&nbsp;danRer7</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2011-12-02</TD><TD ALIGN=RIGHT>22.823%</TD>
  <TD ALIGN=RIGHT>7.365%</TD></TR>
<TR>
  <TH>Coelacanth&nbsp;latCha1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2012-01-13</TD><TD ALIGN=RIGHT>13.735%</TD>
  <TD ALIGN=RIGHT>2.878%</TD></TR>

</TABLE>