Ce10 conservation lastz parameters: Difference between revisions
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(fix default indication of L and H parameters) |
(fixup default L value) |
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<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( | <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> | ||
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<TR> | <TR> | ||
<TH>C. briggsae cb4</TH> | <TH>C. briggsae cb4</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caeSp91</TH> | <TH>C. sp. 9 ju1422 caeSp91</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caeRem4</TH> | <TH>C. remanei caeRem4</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caeSp111</TH> | <TH>C. sp. 11 ju1373 caeSp111</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caePb3</TH> | <TH>C. brenneri caePb3</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caeSp71</TH> | <TH>C. sp. 7 ju1286 caeSp71</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caeJap4</TH> | <TH>C. japonica caeJap4</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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 caeAng1</TH> | <TH>C. angaria caeAng1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><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
- C. elegans 9-way Ce10 Genome size statistics
- C. elegans 9-way Ce10 conservation alignment
- all other UCSC Multiple Alignments
| The default scoring matrix is: | The HoxD55 scoring matrix is: | The human-chimp.v2 scoring matrix is: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
O=400 E=30 |
O=400 E=30 |
O=600 E=150 |
do not edit, automatically generated table
| query | abridged repeats(no) |
M(0) | K(3000) | L(3000) | Q | Y(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 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-07 | 39.386% | 36.190% |
| C. sp. 9 ju1422 caeSp91 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-07 | 42.169% | 36.281% |
| C. remanei caeRem4 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-07 | 41.722% | 33.467% |
| C. sp. 11 ju1373 caeSp111 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-07 | 37.876% | 47.371% |
| C. brenneri caePb3 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-08 | 40.644% | 32.339% |
| C. sp. 7 ju1286 caeSp71 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-07 | 40.236% | 35.479% |
| C. japonica caeJap4 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-07 | 27.737% | 19.557% |
| C. angaria caeAng1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-06-08 | 17.625% | 23.396% |
