GeoFor1 conservation lastz parameters: Difference between revisions
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<TR> | <TR> | ||
<TH>Zebra finch taeGut1</TH> | <TH>Zebra finch taeGut1</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-07-31</TD><TD ALIGN=RIGHT>92.532%</TD> | <TD>2012-07-31</TD><TD ALIGN=RIGHT>92.532%</TD> | ||
<TD ALIGN=RIGHT>92.089%</TD></TR> | <TD ALIGN=RIGHT>92.089%</TD></TR> | ||
<TR> | |||
<TH>Budgerigar melUnd1</TH> | |||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | |||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | |||
<TD>2012-07-29</TD><TD ALIGN=RIGHT>80.650%</TD> | |||
<TD ALIGN=RIGHT>76.598%</TD></TR> | |||
<TR> | <TR> | ||
<TH>Chicken galGal4</TH> | <TH>Chicken galGal4</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-07-30</TD><TD ALIGN=RIGHT>70.718%</TD> | <TD>2012-07-30</TD><TD ALIGN=RIGHT>70.718%</TD> | ||
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<TR> | <TR> | ||
<TH>Turkey melGal1</TH> | <TH>Turkey melGal1</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | <TD>9400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-07-29</TD><TD ALIGN=RIGHT>67.079%</TD> | <TD>2012-07-29</TD><TD ALIGN=RIGHT>67.079%</TD> | ||
<TD ALIGN=RIGHT>72.625%</TD></TR> | <TD ALIGN=RIGHT>72.625%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Human hg19</TH> | <TH>Human hg19</TH> | ||
Latest revision as of 21:11, 15 August 2012
See Also
- Medium ground finch 7-way GeoFor1 Genome size statistics
- Medium ground finch 7-way GeoFor1 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 geoFor1 matched (chainLink table) |
% of query matched (chainLinkGeoFor1) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Zebra finch taeGut1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-31 | 92.532% | 92.089% |
| Budgerigar melUnd1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-29 | 80.650% | 76.598% |
| Chicken galGal4 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-30 | 70.718% | 72.077% |
| Turkey melGal1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-29 | 67.079% | 72.625% |
| Human hg19 | no | 0 | 2200 | 10000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-29 | 8.504% | 3.503% |
| Mouse mm10 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-07-29 | 7.709% | 3.543% |
