Rn5 conservation lastz parameters
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See Also
- Rat 13-way Rn5 Genome size statistics
- Rat 13-way Rn5 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 rn5 matched (chainLink table) |
% of query matched (chainLinkRn5) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Mouse mm10 | yes | 0 | 3000 | 3000 | mouse_rat_2.q | 5000 | lastz-distrib-1.03.02/bin/lastz | 55 | 2000 | 600 | 2 | 2012-03-27 | 70.278% | 67.353% |
| Guinea pig cavPor3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-12-01 | 29.127% | 28.164% |
| Human hg19 | no | 0 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2012-06-28 | 36.299% | 31.662% |
| Chimp panTro4 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-12-01 | 35.616% | 31.061% |
| Rhesus rheMac3 | no | 254 | 3000 | 3000 | default | 9400 | lastz | 30 | 2000 | 400 | 1 | 2012-07-11 | 34.835% | 32.516% |
| Dog canFam3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-12-03 | 29.852% | 30.695% |
| Panda ailMel1 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-12-01 | 31.818% | 34.580% |
| Cow bosTau7 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-12-01 | 26.820% | 24.528% |
| Opossum monDom5 | no | 254 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-12-04 | 9.694% | 6.902% |
| Chicken galGal4 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-11-30 | 3.788% | 7.860% |
| Turkey melGal1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-11-14 | 3.630% | 7.975% |
| Zebrafish danRer7 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-11-14 | 2.588% | 4.824% |
