View source for GalVar1 6-way conservation lastz parameters

==See Also==

<UL>
<LI>Malayan flying lemur 6-way [[GalVar1 6-way Genome size statistics]]</LI>
<LI>Malayan flying lemur 6-way [[GalVar1 6-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==
{| border='1' style='border-collapse:collapse' class='wikitable sortable'
|+ Malayan flying lemur/galVar1 6-way conservation alignment
! query
! abridged<br>repeats(no)
! M(0)
! K(3000)
! L(3000)
! Q
! Y(9400)
! program<br>run
! E(30)
! H(0)
! O(400)
! T(1)
! chain&nbsp;table<br>date
! %&nbsp;of&nbsp;galVar1<br>matched<br>(chainLink&nbsp;table)
! %&nbsp;of&nbsp;query<br>matched<br>(chainLinkGalVar1)
|-
! Chinese tree shrew&nbsp;tupChi1
| no
| 254 
| 3000
| 3000
| default
| 9400
| lastz-distrib-1.03.66/bin/lastz
| 30
| 2000
| 400
| 1
| 2017-03-09
| 53.211%
| 52.252%
|-
! Tree shrew&nbsp;tupBel1
| no
| 254 
| 3000
| 3000
| default
| 9400
| lastz-distrib-1.03.66/bin/lastz
| 30
| 2000
| 400
| 1
| 2016-04-26
| 41.502%
| 50.947%
|-
! Human&nbsp;hg38
| no
| 254
| 3000
| 3000
| default
| 9400
| lastz-distrib-1.03.66/bin/lastz
| 30
| 2000
| 400
| 1
| 2016-04-26
| 64.881%
| 57.036%
|-
! Guinea pig&nbsp;cavPor3
| no
| 0
| 3000
| 3000
| default
| 9400
| lastz-distrib-1.03.54/bin/lastz
| 30
| 2000
| 400
| 1
| 2016-04-18
| 48.448%
| 48.820%
|-
! Mouse&nbsp;mm10
| no
| 254
| 3000
| 3000
| default
| 9400
| lastz-distrib-1.03.66/bin/lastz
| 30
| 2000
| 400
| 1
| 2016-04-26
| 35.972%
| 35.618%
|}