View source for TarSyr2 20-way conservation lastz parameters

==See Also==

<UL>
<LI>Tarsier 20-way [[TarSyr2 20-way Genome size statistics]]</LI>
<LI>Tarsier 20-way [[TarSyr2 20-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;tarSyr2<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkTarSyr2)</TH>
</TR>
<TR>
  <TH>Squirrel monkey&nbsp;saiBol1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>saiBol1.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-15</TD><TD ALIGN=RIGHT>48.208%</TD>
  <TD ALIGN=RIGHT>59.766%</TD></TR>
<TR>
  <TH>Marmoset&nbsp;calJac3</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>calJac3.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-13</TD><TD ALIGN=RIGHT>48.629%</TD>
  <TD ALIGN=RIGHT>55.800%</TD></TR>
<TR>
  <TH>Gorilla&nbsp;gorGor3</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>gorGor3.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-13</TD><TD ALIGN=RIGHT>50.262%</TD>
  <TD ALIGN=RIGHT>56.297%</TD></TR>
<TR>
  <TH>Gibbon&nbsp;nomLeu3</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>nomLeu3.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-13</TD><TD ALIGN=RIGHT>50.545%</TD>
  <TD ALIGN=RIGHT>56.775%</TD></TR>
<TR>
  <TH>Orangutan&nbsp;ponAbe2</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>ponAbe2.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-13</TD><TD ALIGN=RIGHT>51.302%</TD>
  <TD ALIGN=RIGHT>55.431%</TD></TR>
<TR>
  <TH>Human&nbsp;hg38</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-13</TD><TD ALIGN=RIGHT>52.305%</TD>
  <TD ALIGN=RIGHT>56.022%</TD></TR>
<TR>
  <TH>Bonobo&nbsp;panPan1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>panPan1.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-16</TD><TD ALIGN=RIGHT>52.289%</TD>
  <TD ALIGN=RIGHT>59.834%</TD></TR>
<TR>
  <TH>Chimp&nbsp;panTro4</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>panTro4.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-15</TD><TD ALIGN=RIGHT>51.284%</TD>
  <TD ALIGN=RIGHT>56.630%</TD></TR>
<TR>
  <TH>Proboscis monkey&nbsp;nasLar1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>nasLar1.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-16</TD><TD ALIGN=RIGHT>47.164%</TD>
  <TD ALIGN=RIGHT>61.165%</TD></TR>
<TR>
  <TH>Golden snub-nosed monkey&nbsp;rhiRox1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>rhiRox1.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2015-02-24</TD><TD ALIGN=RIGHT>51.539%</TD>
  <TD ALIGN=RIGHT>56.545%</TD></TR>
<TR>
  <TH>Crab-eating macaque&nbsp;macFas5</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>macFas5.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-16</TD><TD ALIGN=RIGHT>51.814%</TD>
  <TD ALIGN=RIGHT>57.176%</TD></TR>
<TR>
  <TH>Rhesus&nbsp;rheMac3</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>rheMac3.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-16</TD><TD ALIGN=RIGHT>50.710%</TD>
  <TD ALIGN=RIGHT>59.428%</TD></TR>
<TR>
  <TH>Baboon&nbsp;papAnu2</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>papAnu2.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-15</TD><TD ALIGN=RIGHT>51.652%</TD>
  <TD ALIGN=RIGHT>56.346%</TD></TR>
<TR>
  <TH>Green monkey&nbsp;chlSab2</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>chlSab2.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-16</TD><TD ALIGN=RIGHT>51.691%</TD>
  <TD ALIGN=RIGHT>58.191%</TD></TR>
<TR>
  <TH>Mouse lemur&nbsp;micMur1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>micMur1.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-13</TD><TD ALIGN=RIGHT>38.087%</TD>
  <TD ALIGN=RIGHT>64.649%</TD></TR>
<TR>
  <TH>Bushbaby&nbsp;otoGar3</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>otoGar3.tarSyr2.tuning.Q.txt</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD>
  <TD>2014-12-15</TD><TD ALIGN=RIGHT>44.814%</TD>
  <TD ALIGN=RIGHT>59.044%</TD></TR>
<TR>
  <TH>Dog&nbsp;canFam3</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-04-05</TD><TD ALIGN=RIGHT>44.555%</TD>
  <TD ALIGN=RIGHT>57.932%</TD></TR>
<TR>
  <TH>Tree shrew&nbsp;tupBel1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-04-02</TD><TD ALIGN=RIGHT>31.268%</TD>
  <TD ALIGN=RIGHT>47.221%</TD></TR>
<TR>
  <TH>Mouse&nbsp;mm10</TH>
  <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
  <TD>9400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-04-02</TD><TD ALIGN=RIGHT>26.433%</TD>
  <TD ALIGN=RIGHT>32.301%</TD></TR>
</TABLE>