Ce9 conservation lastz parameters: Difference between revisions

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<LI>[[Ce9 Genome size statistics]]</LI>
<LI>[[Ce9 Genome size statistics]]</LI>
<LI>[[Ce9 conservation alignment]]</LI>
<LI>[[Ce9 conservation alignment]]</LI>
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 Andy's alignment notes]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
</UL>
</UL>


<TABLE BORDER=0>
<TABLE BORDER=0>
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</TR>
</TR>
<TR>
<TR>
   <TH>C. briggsae&nbsp;cb3</TH>
   <TH>C.&nbsp;briggsae cb3</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>39.763%</TD></TR>
   <TD ALIGN=RIGHT>39.763%</TD></TR>
<TR>
<TR>
   <TH>C. remanei&nbsp;caeRem3</TH>
   <TH>C.&nbsp;remanei caeRem3</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>33.467%</TD></TR>
   <TD ALIGN=RIGHT>33.467%</TD></TR>
<TR>
<TR>
   <TH>C. brenneri&nbsp;caePb2</TH>
   <TH>C.&nbsp;brenneri caePb2</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000 </TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000 </TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>32.313%</TD></TR>
   <TD ALIGN=RIGHT>32.313%</TD></TR>
<TR>
<TR>
   <TH>C. japonica&nbsp;caeJap3</TH>
   <TH>C.&nbsp;japonica caeJap3</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>19.464%</TD></TR>
   <TD ALIGN=RIGHT>19.464%</TD></TR>
<TR>
<TR>
   <TH>H. contortus&nbsp;haeCon1</TH>
   <TH>H.&nbsp;contortus haeCon1</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>3.178%</TD></TR>
   <TD ALIGN=RIGHT>3.178%</TD></TR>
<TR>
<TR>
   <TH>P. pacificus&nbsp;priPac2</TH>
   <TH>P.&nbsp;pacificus priPac2</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>4.692%</TD></TR>
   <TD ALIGN=RIGHT>4.692%</TD></TR>
<TR>
<TR>
   <TH>M. hapla&nbsp;melHap1</TH>
   <TH>M.&nbsp;hapla melHap1</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>6.849%</TD></TR>
   <TD ALIGN=RIGHT>6.849%</TD></TR>
<TR>
<TR>
   <TH>M. incognita&nbsp;melInc1</TH>
   <TH>M.&nbsp;incognita melInc1</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>5.166%</TD></TR>
   <TD ALIGN=RIGHT>5.166%</TD></TR>
<TR>
<TR>
   <TH>B. malayi&nbsp;bruMal1</TH>
   <TH>B.&nbsp;malayi bruMal1</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <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>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>

Latest revision as of 23:45, 31 May 2011

See Also:


The default
scoring matrix is:
 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

O=400 E=30

lastz parameters

Automatically generated table, do not edit

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 ce9
matched
(chainLink table)
% of query
matched
(chainLinkCe9)
C. briggsae cb3 no5030003000default 9400lastz3020004001 2010-09-2042.300% 39.763%
C. remanei caeRem3 no5030003000default 9400lastz3020004001 2010-09-2041.722% 33.467%
C. brenneri caePb2 no5030003000default 9400lastz302000 4001 2010-09-2040.677% 32.313%
C. japonica caeJap3 no5030003000default 9400lastz3020004001 2010-09-2227.580% 19.464%
H. contortus haeCon1 no5030003000default 9400lastz3020004001 2010-09-237.463% 3.178%
P. pacificus priPac2 no5030003000default 9400lastz3020004001 2010-09-295.862% 4.692%
M. hapla melHap1 no5030003000default 9400lastz3020004001 2010-09-223.922% 6.849%
M. incognita melInc1 no5030003000default 9400lastz3020004001 2010-09-223.301% 5.166%
B. malayi bruMal1 no5030003000default 9400lastz3020004001 2010-09-224.790% 5.457%