Ce10 conservation lastz parameters: Difference between revisions

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(fix default indication of L and H parameters)
(fixup default L value)
 
Line 45: Line 45:
   <TH>abridged<BR>repeats(no)</TH>
   <TH>abridged<BR>repeats(no)</TH>
   <TH>M(0)</TH><TH>K(3000)</TH>
   <TH>M(0)</TH><TH>K(3000)</TH>
   <TH>L(2200)</TH><TH>Q</TH><TH>Y(9400)</TH>
   <TH>L(3000)</TH><TH>Q</TH><TH>Y(9400)</TH>
   <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(2000)</TH>
   <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(2000)</TH>
   <TH>O(400)</TH><TH>T(1)</TH>
   <TH>O(400)</TH><TH>T(1)</TH>
Line 54: Line 54:
<TR>
<TR>
   <TH>C. briggsae&nbsp;cb4</TH>
   <TH>C. briggsae&nbsp;cb4</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>39.386%</TD>
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<TR>
<TR>
   <TH>C. sp. 9 ju1422&nbsp;caeSp91</TH>
   <TH>C. sp. 9 ju1422&nbsp;caeSp91</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>42.169%</TD>
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<TR>
<TR>
   <TH>C. remanei&nbsp;caeRem4</TH>
   <TH>C. remanei&nbsp;caeRem4</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>41.722%</TD>
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<TR>
<TR>
   <TH>C. sp. 11 ju1373&nbsp;caeSp111</TH>
   <TH>C. sp. 11 ju1373&nbsp;caeSp111</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>37.876%</TD>
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<TR>
<TR>
   <TH>C. brenneri&nbsp;caePb3</TH>
   <TH>C. brenneri&nbsp;caePb3</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD>
   <TD>2011-06-08</TD><TD ALIGN=RIGHT>40.644%</TD>
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<TR>
<TR>
   <TH>C. sp. 7 ju1286&nbsp;caeSp71</TH>
   <TH>C. sp. 7 ju1286&nbsp;caeSp71</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>40.236%</TD>
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<TR>
<TR>
   <TH>C. japonica&nbsp;caeJap4</TH>
   <TH>C. japonica&nbsp;caeJap4</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD>
   <TD>2011-06-07</TD><TD ALIGN=RIGHT>27.737%</TD>
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<TR>
<TR>
   <TH>C. angaria&nbsp;caeAng1</TH>
   <TH>C. angaria&nbsp;caeAng1</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>2200</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>
   <TD>2011-06-08</TD><TD ALIGN=RIGHT>17.625%</TD>
   <TD>2011-06-08</TD><TD ALIGN=RIGHT>17.625%</TD>

Latest revision as of 21:20, 15 August 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(2000) O(400)T(1) chain table
date
% of ce10
matched
(chainLink table)
% of query
matched
(chainLinkCe10)
C. briggsae cb4 no5030003000default 9400lastz3020004001 2011-06-0739.386% 36.190%
C. sp. 9 ju1422 caeSp91 no5030003000default 9400lastz3020004001 2011-06-0742.169% 36.281%
C. remanei caeRem4 no5030003000default 9400lastz3020004001 2011-06-0741.722% 33.467%
C. sp. 11 ju1373 caeSp111 no5030003000default 9400lastz3020004001 2011-06-0737.876% 47.371%
C. brenneri caePb3 no5030003000default 9400lastz3020004001 2011-06-0840.644% 32.339%
C. sp. 7 ju1286 caeSp71 no5030003000default 9400lastz3020004001 2011-06-0740.236% 35.479%
C. japonica caeJap4 no5030003000default 9400lastz3020004001 2011-06-0727.737% 19.557%
C. angaria caeAng1 no5030003000default 9400lastz3020004001 2011-06-0817.625% 23.396%