Hg38 20-way conservation lastz parameters: Difference between revisions
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(updated with new alignments for canFam3 rheMac3 and mm10) |
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<TH>Rhesus rheMac3</TH> | <TH>Rhesus rheMac3</TH> | ||
<TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | <TD>no</TD><TD>254</TD><TD>4500</TD><TD>3000</TD><TD>human_chimp.v2.q</TD> | ||
<TD>15000</TD><TD>lastz-distrib-1.03. | <TD>15000</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>150</TD><TD>2000</TD><TD>600</TD><TD>2</TD> | ||
<TD> | <TD>2015-04-09</TD><TD ALIGN=RIGHT>80.828%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>88.220%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Baboon papAnu2</TH> | <TH>Baboon papAnu2</TH> | ||
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<TH>Dog canFam3</TH> | <TH>Dog canFam3</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03. | <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2015-04-10</TD><TD ALIGN=RIGHT>50.395%</TD> | ||
<TD ALIGN=RIGHT>60. | <TD ALIGN=RIGHT>60.861%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Tree shrew tupBel1</TH> | <TH>Tree shrew tupBel1</TH> | ||
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<TH>Mouse mm10</TH> | <TH>Mouse mm10</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>3000</TD><TD>default</TD> | ||
<TD>9400</TD><TD>lastz-distrib-1.03. | <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD> | <TD>2015-04-09</TD><TD ALIGN=RIGHT>31.653%</TD> | ||
<TD ALIGN=RIGHT>35. | <TD ALIGN=RIGHT>35.372%</TD></TR> | ||
</TABLE> | </TABLE> | ||
Latest revision as of 04:43, 16 April 2015
See Also
- Human 20-way Hg38 20-way Genome size statistics
- Human 20-way Hg38 20-way 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 hg38 matched (chainLink table) |
% of query matched (chainLinkHg38) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Chimp panTro4 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-05-27 | 93.112% | 95.664% |
| Bonobo panPan1 | no | 254 | 3000 | 3000 | hg38.panPan1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-11 | 92.929% | 97.795% |
| Gorilla gorGor3 | no | 254 | 3000 | 3000 | hg38.gorGor3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 88.005% | 91.695% |
| Orangutan ponAbe2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-09-02 | 89.187% | 89.656% |
| Gibbon nomLeu3 | no | 254 | 3000 | 3000 | hg38.nomLeu3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-12 | 86.379% | 90.470% |
| Proboscis monkey nasLar1 | no | 254 | 3000 | 3000 | hg38.nasLar1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 74.541% | 89.972% |
| Golden snub-nosed monkey rhiRox1 | no | 254 | 3000 | 3000 | hg38.rhiRox1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-23 | 85.109% | 86.629% |
| Crab-eating macaque macFas5 | no | 254 | 3000 | 3000 | hg38.macFas5.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-14 | 85.675% | 87.749% |
| Rhesus rheMac3 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.66/bin/lastz | 150 | 2000 | 600 | 2 | 2015-04-09 | 80.828% | 88.220% |
| Baboon papAnu2 | no | 254 | 3000 | 3000 | hg38.papAnu2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 84.179% | 84.502% |
| Squirrel monkey saiBol1 | no | 254 | 3000 | 3000 | hg38.saiBol1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 70.565% | 81.466% |
| Green monkey chlSab2 | no | 254 | 4500 | 3000 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.52/bin/lastz | 150 | 2000 | 600 | 2 | 2014-07-11 | 84.393% | 88.264% |
| Marmoset calJac3 | no | 254 | 3000 | 3000 | hg38.calJac3.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 71.709% | 76.757% |
| Tarsier tarSyr2 | no | 50 | 3000 | 3000 | hg38.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-12 | 56.022% | 52.305% |
| Mouse lemur micMur1 | no | 254 | 3000 | 3000 | hg38.micMur1.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2015-03-22 | 42.653% | 67.655% |
| Bushbaby otoGar3 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 2 | 2015-02-23 | 53.196% | 64.899% |
| Dog canFam3 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-10 | 50.395% | 60.861% |
| Tree shrew tupBel1 | no | 254 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 1 | 2015-03-27 | 35.019% | 49.422% |
| Mouse mm10 | no | 0 | 3000 | 3000 | default | 9400 | lastz-distrib-1.03.66/bin/lastz | 30 | 2000 | 400 | 1 | 2015-04-09 | 31.653% | 35.372% |
