Fr3 conservation lastz parameters: Difference between revisions
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(updated to 8-way) |
(updated to 8-way) |
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| Line 2: | Line 2: | ||
<UL> | <UL> | ||
<LI>Fugu | <LI>Fugu 8-way [[Fr3 Genome size statistics]]</LI> | ||
<LI>Fugu | <LI>Fugu 8-way [[Fr3 conservation alignment]]</LI> | ||
<LI>all other [[UCSC Multiple Alignments]]</LI> | <LI>all other [[UCSC Multiple Alignments]]</LI> | ||
</UL> | </UL> | ||
Latest revision as of 22:26, 29 February 2012
See Also
- Fugu 8-way Fr3 Genome size statistics
- Fugu 8-way Fr3 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 fr3 matched (chainLink table) |
% of query matched (chainLinkFr3) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Tetraodon tetNig2 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-12-01 | 70.912% | 80.674% |
| Nile tilapia oreNil1 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-12-02 | 57.240% | 30.736% |
| Stickleback gasAcu1 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-12-02 | 55.527% | 48.038% |
| Atlantic cod gadMor1 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2012-01-14 | 30.327% | 19.051% |
| Medaka oryLat2 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-12-02 | 43.863% | 25.905% |
| Zebrafish danRer7 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2011-12-02 | 22.823% | 7.365% |
| Coelacanth latCha1 | no | 50 | 3000 | 3000 | HoxD55.q | 9400 | lastz | 30 | 2000 | 400 | 1 | 2012-01-13 | 13.735% | 2.878% |
