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>[[ | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
<TABLE BORDER=0> | <TABLE BORDER=0> | ||
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</TR> | </TR> | ||
<TR> | <TR> | ||
<TH>C. | <TH>C. 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. | <TH>C. 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. | <TH>C. 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. | <TH>C. 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. | <TH>H. 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. | <TH>P. 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. | <TH>M. 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. | <TH>M. 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. | <TH>B. 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: | |||||||||||||||||||||||||
O=400 E=30 |
lastz parameters
Automatically generated table, do not edit
| query | abridged repeats(no) |
M(40M) | K(3000) | L(3000) | Q | Y(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 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-20 | 42.300% | 39.763% |
| C. remanei caeRem3 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-20 | 41.722% | 33.467% |
| C. brenneri caePb2 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-20 | 40.677% | 32.313% |
| C. japonica caeJap3 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-22 | 27.580% | 19.464% |
| H. contortus haeCon1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-23 | 7.463% | 3.178% |
| P. pacificus priPac2 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-29 | 5.862% | 4.692% |
| M. hapla melHap1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-22 | 3.922% | 6.849% |
| M. incognita melInc1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-22 | 3.301% | 5.166% |
| B. malayi bruMal1 | no | 50 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2010-09-22 | 4.790% | 5.457% |
