View source for DanRer10 12-way conservation lastz parameters

==See Also==

<UL>
<LI>Zebrafish 12-way [[DanRer10 12-way Genome size statistics]]</LI>
<LI>Zebrafish 12-way [[DanRer10 12-way 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;danRer10<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkDanRer10)</TH>
</TR>
<TR>
  <TH>Stickleback&nbsp;gasAcu1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-02-10</TD><TD ALIGN=RIGHT>9.814%</TD>
  <TD ALIGN=RIGHT>27.557%</TD></TR>
<TR>
  <TH>Spotted gar&nbsp;lepOcu1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.04.00/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2020-02-25</TD><TD ALIGN=RIGHT>8.409%</TD>
  <TD ALIGN=RIGHT>11.294%</TD></TR>
<TR>
  <TH>Tetraodon&nbsp;tetNig2</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-02-09</TD><TD ALIGN=RIGHT>6.063%</TD>
  <TD ALIGN=RIGHT>23.344%</TD></TR>
<TR>
  <TH>Fugu&nbsp;fr3</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-02-09</TD><TD ALIGN=RIGHT>7.080%</TD>
  <TD ALIGN=RIGHT>22.699%</TD></TR>
<TR>
  <TH>Medaka&nbsp;oryLat2</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2017-02-09</TD><TD ALIGN=RIGHT>9.640%</TD>
  <TD ALIGN=RIGHT>17.684%</TD></TR>
<TR>
  <TH>X. tropicalis&nbsp;xenTro9</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.04.00/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2020-02-25</TD><TD ALIGN=RIGHT>6.731%</TD>
  <TD ALIGN=RIGHT>7.029%</TD></TR>
<TR>
  <TH>Chicken&nbsp;galGal6</TH>
  <TD>no</TD><TD>254</TD><TD>2200</TD><TD>4000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.04.00/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2020-02-25</TD><TD ALIGN=RIGHT>5.871%</TD>
  <TD ALIGN=RIGHT>6.171%</TD></TR>
<TR>
  <TH>Elephant shark&nbsp;calMil1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.04.00/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2020-02-25</TD><TD ALIGN=RIGHT>5.599%</TD>
  <TD ALIGN=RIGHT>7.088%</TD></TR>
<TR>
  <TH>Human&nbsp;hg38</TH>
  <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-02-09</TD><TD ALIGN=RIGHT>7.110%</TD>
  <TD ALIGN=RIGHT>3.357%</TD></TR>
<TR>
  <TH>Mouse&nbsp;mm10</TH>
  <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-09-18</TD><TD ALIGN=RIGHT>5.228%</TD>
  <TD ALIGN=RIGHT>2.769%</TD></TR>
<TR>
  <TH>Coelacanth&nbsp;latCha1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz-distrib-1.04.00/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2020-02-25</TD><TD ALIGN=RIGHT>6.319%</TD>
  <TD ALIGN=RIGHT>4.504%</TD></TR>
</TABLE>