View source for CalJac3 conservation lastz parameters

==See Also==

<UL>
<LI>Marmoset 13-way [[Marmoset_calJac3_13-way_size_statistics|CalJac3 Genome size statistics]]</LI>
<LI>Marmoset 13-way [[CalJac3 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;calJac3<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkCalJac3)</TH>
</TR>
<TR>
  <TH>Orangutan&nbsp;ponAbe2</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2010-02-12</TD><TD ALIGN=RIGHT>71.893%</TD>
  <TD ALIGN=RIGHT>67.448%</TD></TR>
<TR>
  <TH>Human&nbsp;hg19</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2010-02-11</TD><TD ALIGN=RIGHT>73.768%</TD>
  <TD ALIGN=RIGHT>70.654%</TD></TR>
<TR>
  <TH>Chimp&nbsp;panTro2</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2010-02-11</TD><TD ALIGN=RIGHT>72.304%</TD>
  <TD ALIGN=RIGHT>69.302%</TD></TR>
<TR>
  <TH>Gorilla&nbsp;gorGor2</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-23</TD><TD ALIGN=RIGHT>76.343%</TD>
  <TD ALIGN=RIGHT>75.481%</TD></TR>
<TR>
  <TH>Rhesus&nbsp;rheMac2</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2010-02-12</TD><TD ALIGN=RIGHT>69.625%</TD>
  <TD ALIGN=RIGHT>70.711%</TD></TR>
<TR>
  <TH>Baboon&nbsp;papHam1</TH>
  <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD>
  <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>0</TD><TD>600</TD><TD>2</TD>
  <TD>2010-02-18</TD><TD ALIGN=RIGHT>70.053%</TD>
  <TD ALIGN=RIGHT>69.607%</TD></TR>
<TR>
  <TH>Tarsier&nbsp;tarSyr1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-24</TD><TD ALIGN=RIGHT>46.729%</TD>
  <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
  <TH>Mouse lemur&nbsp;micMur1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-21</TD><TD ALIGN=RIGHT>45.726%</TD>
  <TD ALIGN=RIGHT>67.145%</TD></TR>
<TR>
  <TH>Bushbaby&nbsp;otoGar1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-21</TD><TD ALIGN=RIGHT>42.743%</TD>
  <TD ALIGN=RIGHT>58.837%</TD></TR>
<TR>
  <TH>Dog&nbsp;canFam2</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-14</TD><TD ALIGN=RIGHT>50.766%</TD>
  <TD ALIGN=RIGHT>57.162%</TD></TR>
<TR>
  <TH>Mouse&nbsp;mm9</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-14</TD><TD ALIGN=RIGHT>31.310%</TD>
  <TD ALIGN=RIGHT>32.815%</TD></TR>
<TR>
  <TH>Opossum&nbsp;monDom5</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
  <TD>2010-02-14</TD><TD ALIGN=RIGHT>7.906%</TD>
  <TD ALIGN=RIGHT>6.174%</TD></TR>

</TABLE>