DanRer7 conservation lastz parameters: Difference between revisions

From genomewiki
Jump to navigationJump to search
(updated for hg19 and mm9)
(only need HoxD55 matrix)
Line 13: Line 13:


<TABLE BORDER=0>
<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<TR><TD>The HoxD55<BR>scoring matrix is:</TD></TR>
<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>
<TR><TD><TABLE BORDER=1>
<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>&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>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
Line 33: Line 23:
</TABLE>
</TABLE>
O=400 E=30
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>
</TD>
</TR></TABLE>
</TR></TABLE>

Revision as of 19:50, 4 February 2011

See Also:

The HoxD55
scoring matrix is:
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

do not edit, automatically generated table

query abridged
repeats(no)		 M(40M)K(3000) L(3000)QY(9400) program
run		E(30)H(0) O(400)T(1) chain table
date		 % of danRer7
matched
(chainLink table)		 % of query
matched
(chainLinkDanRer7)
Stickleback gasAcu1 no5030003000HoxD55.q 9400lastz3004001 2010-12-1710.270% 27.522%
Medaka oryLat2 no5030003000HoxD55.q 9400lastz3004001 2010-12-1710.032% 17.780%
Tetraodon tetNig2 no5030003000HoxD55.q 9400lastz3004001 2010-12-176.273% 23.571%
Fugu fr2 no5030003000HoxD55.q 9400lastz3004001 2010-12-217.363% 20.360%
X. tropicalis xenTro2 no40M22006000HoxD55.q 3400lastz3020004001 2010-12-176.428% 6.610%
Mouse mm9 no40M22006000HoxD55.q 3400lastz3020004001 2010-12-175.104% 2.602%
Human hg19 no40M22006000HoxD55.q 3400lastz3020004001 2010-12-206.151% 2.790%
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=DanRer7_conservation_lastz_parameters&oldid=12729"