Mm10 conservation lastz parameters: Difference between revisions
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(updated data with altered species list) |
(updated data) |
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<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</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>2012-03-22</TD><TD ALIGN=RIGHT> | <TD>2012-03-22</TD><TD ALIGN=RIGHT>18.019%</TD> | ||
<TD ALIGN=RIGHT>23.687%</TD></TR> | |||
<TR> | |||
<TH>Manatee triMan1</TH> | |||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</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>2012-03-30</TD><TD ALIGN=RIGHT>26.546%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | <TR> | ||
<TH>Megabat pteVam1</TH> | <TH>Megabat pteVam1</TH> | ||
<TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
| Line 291: | Line 294: | ||
<TR> | <TR> | ||
<TH>Opossum monDom5</TH> | <TH>Opossum monDom5</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-03-30</TD><TD ALIGN=RIGHT>9.584%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Tasmanian devil sarHar1</TH> | <TH>Tasmanian devil sarHar1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-03-30</TD><TD ALIGN=RIGHT>8.479%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Budgerigar melUnd1</TH> | <TH>Budgerigar melUnd1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-03-30</TD><TD ALIGN=RIGHT>3.589%</TD> | |||
<TD ALIGN=RIGHT>7.350%</TD></TR> | |||
<TR> | |||
<TH>Platypus ornAna1</TH> | <TH>Platypus ornAna1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-03-30</TD><TD ALIGN=RIGHT>5.348%</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Painted turtle chrPic1</TH> | <TH>Painted turtle chrPic1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD> | ||
</TR><TR> | <TD>3400</TD><TD>lastz-distrib-1.03.02/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD> | ||
<TD>2012-03-30</TD><TD ALIGN=RIGHT>4.731%</TD> | |||
<TD ALIGN=RIGHT>5.488%</TD></TR> | |||
<TR> | |||
<TH>Chicken galGal4</TH> | <TH>Chicken galGal4</TH> | ||
<TD COLSPAN=14 ALIGN=center>TBD</TD> | <TD COLSPAN=14 ALIGN=center>TBD</TD> | ||
Revision as of 17:22, 2 April 2012
See Also
- Mouse 60-way Mm10 Genome size statistics
- Mouse 60-way Mm10 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 mm10 matched (chainLink table) |
% of query matched (chainLinkMm10) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Rat rn4 | no | 0 | 4500 | 2200 | human_chimp.v2.q | 15000 | lastz-distrib-1.03.02/bin/lastz | 150 | 2000 | 600 | 2 | 2012-03-08 | 54.645% | 56.348% |
| Squirrel speTri2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 34.217% | 39.244% |
| Mouse lemur micMur1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-13 | 26.636% | 37.574% |
| Kangaroo rat dipOrd1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 19.460% | 27.512% |
| Squirrel monkey saiBol1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 32.339% | 33.848% |
| Naked mole-rat hetGla1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 32.163% | 36.427% |
| Human hg19 | yes | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-08 | 38.226% | 35.249% |
| Gorilla gorGor3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-08 | 33.987% | 34.349% |
| Chimp panTro4 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-10 | 34.674% | 31.924% |
| Gibbon nomLeu1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-08 | 34.132% | 32.372% |
| Orangutan ponAbe2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 34.496% | 30.610% |
| Tarsier tarSyr1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-12 | 24.560% | 24.986% |
| Chinese rhesus rheMac3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 33.931% | 33.464% |
| Baboon papHam1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-10 | 33.577% | 32.023% |
| Bushbaby otoGar3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-13 | 29.795% | 32.926% |
| Marmoset calJac3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-09 | 32.450% | 31.301% |
| Horse equCab2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-16 | 34.415% | 37.138% |
| Guinea pig cavPor3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 28.447% | 29.115% |
| Alpaca vicPac1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 22.636% | 31.769% |
| Dolphin turTru1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 28.761% | 32.385% |
| Tree shrew tupBel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 19.766% | 25.144% |
| Pig susScr2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 23.248% | 29.422% |
| Rabbit oryCun2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-17 | 25.248% | 25.677% |
| Sloth choHof1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 18.019% | 23.687% |
| Manatee triMan1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 26.546% | N/A |
| Megabat pteVam1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 27.345% | 38.627% |
| Cat felCat4 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 24.033% | 30.953% |
| Panda ailMel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 30.979% | 35.562% |
| Dog canFam3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 29.144% | 31.624% |
| Elephant loxAfr3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-20 | 25.823% | 21.616% |
| Armadillo dasNov2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-23 | 17.004% | 19.445% |
| Microbat myoLuc2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 24.363% | 33.650% |
| Cow bosTau7 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 26.255% | 25.383% |
| Sheep oviAri1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-22 | 15.341% | 31.925% |
| Pika ochPri2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 14.542% | 19.908% |
| Rock hyrax proCap1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-23 | 15.147% | 16.214% |
| Hedgehog eriEur1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 9.856% | 12.264% |
| Tenrec echTel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 10.947% | 14.117% |
| Shrew sorAra1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 9.382% | 13.569% |
| Wallaby macEug2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-24 | 4.353% | 4.448% |
| Opossum monDom5 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 9.584% | N/A |
| Tasmanian devil sarHar1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 8.479% | N/A |
| Budgerigar melUnd1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 3.589% | 7.350% |
| Platypus ornAna1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 5.348% | N/A |
| Painted turtle chrPic1 | no | 0 | 2200 | 6000 | HoxD55.q | 3400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | 2012-03-30 | 4.731% | 5.488% |
| Chicken galGal4 | TBD | |||||||||||||
| Zebra finch taeGut1 | TBD | |||||||||||||
| Lizard anoCar2 | TBD | |||||||||||||
| Turkey melGal1 | TBD | |||||||||||||
| X. tropicalis xenTro3 | TBD | |||||||||||||
| Coelacanth latCha1 | TBD | |||||||||||||
| Atlantic cod gadMor1 | TBD | |||||||||||||
| Nile tilapia oreNil1 | TBD | |||||||||||||
| Stickleback gasAcu1 | TBD | |||||||||||||
| Fugu fr3 | TBD | |||||||||||||
| Tetraodon tetNig2 | TBD | |||||||||||||
| Zebrafish danRer7 | TBD | |||||||||||||
| Medaka oryLat2 | TBD | |||||||||||||
| Lamprey petMar1 | TBD | |||||||||||||
