GorGor3 conservation lastz parameters: Difference between revisions
From genomewiki
Jump to navigationJump to search
(initial contents from the defCheck.pl script) |
(fixup default L value) |
||
| Line 54: | Line 54: | ||
<TR> | <TR> | ||
<TH>Chimp panTro3</TH> | <TH>Chimp panTro3</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-26</TD><TD ALIGN=RIGHT>89.043%</TD> | <TD>2011-10-26</TD><TD ALIGN=RIGHT>89.043%</TD> | ||
| Line 60: | Line 60: | ||
<TR> | <TR> | ||
<TH>Human hg19</TH> | <TH>Human hg19</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-21</TD><TD ALIGN=RIGHT>91.109%</TD> | <TD>2011-10-21</TD><TD ALIGN=RIGHT>91.109%</TD> | ||
| Line 66: | Line 66: | ||
<TR> | <TR> | ||
<TH>Gibbon nomLeu1</TH> | <TH>Gibbon nomLeu1</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-26</TD><TD ALIGN=RIGHT>83.476%</TD> | <TD>2011-10-26</TD><TD ALIGN=RIGHT>83.476%</TD> | ||
| Line 72: | Line 72: | ||
<TR> | <TR> | ||
<TH>Orangutan ponAbe2</TH> | <TH>Orangutan ponAbe2</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-23</TD><TD ALIGN=RIGHT>86.354%</TD> | <TD>2011-10-23</TD><TD ALIGN=RIGHT>86.354%</TD> | ||
| Line 78: | Line 78: | ||
<TR> | <TR> | ||
<TH>Baboon papHam1</TH> | <TH>Baboon papHam1</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-31</TD><TD ALIGN=RIGHT>79.434%</TD> | <TD>2011-10-31</TD><TD ALIGN=RIGHT>79.434%</TD> | ||
| Line 84: | Line 84: | ||
<TR> | <TR> | ||
<TH>Rhesus rheMac2</TH> | <TH>Rhesus rheMac2</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-23</TD><TD ALIGN=RIGHT>79.244%</TD> | <TD>2011-10-23</TD><TD ALIGN=RIGHT>79.244%</TD> | ||
| Line 90: | Line 90: | ||
<TR> | <TR> | ||
<TH>Marmoset calJac3</TH> | <TH>Marmoset calJac3</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-27</TD><TD ALIGN=RIGHT>68.507%</TD> | <TD>2011-10-27</TD><TD ALIGN=RIGHT>68.507%</TD> | ||
| Line 96: | Line 96: | ||
<TR> | <TR> | ||
<TH>Tarsier tarSyr1</TH> | <TH>Tarsier tarSyr1</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-11-05</TD><TD ALIGN=RIGHT>19.482%</TD> | <TD>2011-11-05</TD><TD ALIGN=RIGHT>19.482%</TD> | ||
| Line 102: | Line 102: | ||
<TR> | <TR> | ||
<TH>Mouse lemur micMur1</TH> | <TH>Mouse lemur micMur1</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-11-03</TD><TD ALIGN=RIGHT>22.908%</TD> | <TD>2011-11-03</TD><TD ALIGN=RIGHT>22.908%</TD> | ||
| Line 108: | Line 108: | ||
<TR> | <TR> | ||
<TH>Bushbaby otoGar1</TH> | <TH>Bushbaby otoGar1</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | <TD>15000</TD><TD>lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD>2011-10-27</TD><TD ALIGN=RIGHT>12.017%</TD> | <TD>2011-10-27</TD><TD ALIGN=RIGHT>12.017%</TD> | ||
Latest revision as of 21:18, 15 August 2012
See Also
- Gorilla 11-way GorGor3 Genome size statistics
- Gorilla 11-way GorGor3 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(0) | O(400) | T(1) | chain table date |
% of gorGor3 matched (chainLink table) |
% of query matched (chainLinkGorGor3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chimp panTro3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-26 | 89.043% | 88.043% |
| Human hg19 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-21 | 91.109% | 89.876% |
| Gibbon nomLeu1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-26 | 83.476% | 84.119% |
| Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-23 | 86.354% | 83.548% |
| Baboon papHam1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-31 | 79.434% | 80.874% |
| Rhesus rheMac2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-23 | 79.244% | 82.188% |
| Marmoset calJac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-27 | 68.507% | 70.073% |
| Tarsier tarSyr1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-11-05 | 19.482% | 20.481% |
| Mouse lemur micMur1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-11-03 | 22.908% | 34.556% |
| Bushbaby otoGar1 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz | 150 | 2000 | 600 | 2 | 2011-10-27 | 12.017% | 17.083% |
