DanRer7 conservation lastz parameters: Difference between revisions
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== | ==see also== | ||
<UL> | <UL> | ||
<LI>[[DanRer7 Genome size statistics]]</LI> | <LI>Zebrafish 8-way [[DanRer7 Genome size statistics]]</LI> | ||
<LI>[[DanRer7 conservation alignment]]</LI> | <LI>Zebrafish 8-way [[DanRer7 conservation alignment]]</LI> | ||
<LI>[[ | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
<TABLE BORDER=0> | <TABLE BORDER=0> | ||
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<TR><TH>query</TH> | <TR><TH>query</TH> | ||
<TH>abridged<BR>repeats(no)</TH> | <TH>abridged<BR>repeats(no)</TH> | ||
<TH>M( | <TH>M(0)</TH><TH>K(3000)</TH> | ||
<TH>L(3000)</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(0)</TH> | <TH>program<BR>run</TH><TH>E(30)</TH><TH>H(0)</TH> | ||
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<TR> | <TR> | ||
<TH>X. tropicalis xenTro2</TH> | <TH>X. tropicalis xenTro2</TH> | ||
<TD>no</TD><TD> | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2010-12-17</TD><TD ALIGN=RIGHT>6.428%</TD> | <TD>2010-12-17</TD><TD ALIGN=RIGHT>6.428%</TD> | ||
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<TR> | <TR> | ||
<TH>Mouse mm9</TH> | <TH>Mouse mm9</TH> | ||
<TD>no</TD><TD> | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2010-12-17</TD><TD ALIGN=RIGHT>5.104%</TD> | <TD>2010-12-17</TD><TD ALIGN=RIGHT>5.104%</TD> | ||
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<TR> | <TR> | ||
<TH>Human hg19</TH> | <TH>Human hg19</TH> | ||
<TD>no</TD><TD> | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
<TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2010-12-20</TD><TD ALIGN=RIGHT>6.151%</TD> | <TD>2010-12-20</TD><TD ALIGN=RIGHT>6.151%</TD> | ||
Latest revision as of 20:20, 19 May 2011
see also
- Zebrafish 8-way DanRer7 Genome size statistics
- Zebrafish 8-way DanRer7 conservation alignment
- all other UCSC Multiple Alignments
| The HoxD55 scoring matrix is: | |||||||||||||||||||||||||
O=400 E=30 |
do not edit, automatically generated table
| query | abridged repeats(no) |
M(0) | K(3000) | L(3000) | Q | Y(9400) | program run | E(30) | H(0) | O(400) | T(1) | chain table date |
% of danRer7 matched (chainLink table) |
% of query matched (chainLinkDanRer7) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Stickleback gasAcu1 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 0 | 400 | 1 | 2010-12-17 | 10.270% | 27.522% |
| Medaka oryLat2 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 0 | 400 | 1 | 2010-12-17 | 10.032% | 17.780% |
| Tetraodon tetNig2 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 0 | 400 | 1 | 2010-12-17 | 6.273% | 23.571% |
| Fugu fr2 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 0 | 400 | 1 | 2010-12-21 | 7.363% | 20.360% |
| X. tropicalis xenTro2 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2010-12-17 | 6.428% | 6.610% |
| Mouse mm9 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2010-12-17 | 5.104% | 2.602% |
| Human hg19 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz | 30 | 2000 | 400 | 1 | 2010-12-20 | 6.151% | 2.790% |
