Fr3 conservation lastz parameters: Difference between revisions

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<UL>
<UL>
<LI>Fugu 6-way [[Fr3 Genome size statistics]]</LI>
<LI>Fugu 8-way [[Fr3 Genome size statistics]]</LI>
<LI>Fugu 6-way [[Fr3 conservation alignment]]</LI>
<LI>Fugu 8-way [[Fr3 conservation alignment]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
</UL>
</UL>
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   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</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>
   <TD>in progress</TD><TD ALIGN=RIGHT>in progress</TD>
   <TD>2011-12-02</TD><TD ALIGN=RIGHT>55.527%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>48.038%</TD></TR>
<TR>
  <TH>Atlantic cod&nbsp;gadMor1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2012-01-14</TD><TD ALIGN=RIGHT>30.327%</TD>
  <TD ALIGN=RIGHT>19.051%</TD></TR>
<TR>
<TR>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TH>Medaka&nbsp;oryLat2</TH>
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   <TD>2011-12-02</TD><TD ALIGN=RIGHT>22.823%</TD>
   <TD>2011-12-02</TD><TD ALIGN=RIGHT>22.823%</TD>
   <TD ALIGN=RIGHT>7.365%</TD></TR>
   <TD ALIGN=RIGHT>7.365%</TD></TR>
<TR>
  <TH>Coelacanth&nbsp;latCha1</TH>
  <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>HoxD55.q</TD>
  <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2012-01-13</TD><TD ALIGN=RIGHT>13.735%</TD>
  <TD ALIGN=RIGHT>2.878%</TD></TR>


</TABLE>
</TABLE>

Latest revision as of 22:26, 29 February 2012

See Also


The default
scoring matrix is:		  The HoxD55
scoring matrix is:		 The human-chimp.v2
scoring matrix is:
 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

O=400 E=30

 
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

 
 ACGT
A90-330-236-356
C-330100-318-236
G-236-318100-330
T-356-236-33090

O=600 E=150

do not edit, automatically generated table

query abridged
repeats(no)		 M(0)K(3000) L(3000)QY(9400) program
run		E(30)H(0) O(400)T(1) chain table
date		 % of fr3
matched
(chainLink table)		 % of query
matched
(chainLinkFr3)
Tetraodon tetNig2 no5030003000HoxD55.q 9400lastz3020004001 2011-12-0170.912% 80.674%
Nile tilapia oreNil1 no5030003000HoxD55.q 9400lastz3020004001 2011-12-0257.240% 30.736%
Stickleback gasAcu1 no5030003000HoxD55.q 9400lastz3020004001 2011-12-0255.527% 48.038%
Atlantic cod gadMor1 no5030003000HoxD55.q 9400lastz3020004001 2012-01-1430.327% 19.051%
Medaka oryLat2 no5030003000HoxD55.q 9400lastz3020004001 2011-12-0243.863% 25.905%
Zebrafish danRer7 no5030003000HoxD55.q 9400lastz3020004001 2011-12-0222.823% 7.365%
Coelacanth latCha1 no5030003000HoxD55.q 9400lastz3020004001 2012-01-1313.735% 2.878%
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