View source for Hg38 4-way conservation lastz parameters

==See Also==

<UL>
<LI>Human 4-way [[Hg38 4-way Genome size statistics]]</LI>
<LI>Human 4-way [[Hg38 4-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;hg38<BR>matched<BR>(chainLink&nbsp;table)</TH>
  <TH>%&nbsp;of&nbsp;query<BR>matched<BR>(chainLinkHg38)</TH>
</TR>
<TR>
  <TH>Malayan flying lemur&nbsp;galVar1</TH>
  <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>default</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>2016-04-26</TD><TD ALIGN=RIGHT>57.036%</TD>
  <TD ALIGN=RIGHT>64.881%</TD></TR>
<TR>
  <TH>Chinese tree shrew&nbsp;tupChi1</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>2015-02-19</TD><TD ALIGN=RIGHT>45.256%</TD>
  <TD ALIGN=RIGHT>50.350%</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-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-04-09</TD><TD ALIGN=RIGHT>31.653%</TD>
  <TD ALIGN=RIGHT>35.372%</TD></TR>
</TABLE>