Mm10 conservation lastz parameters: Difference between revisions
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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> | <TD>2012-03-22</TD><TD ALIGN=RIGHT>in progress</TD> | ||
<TD ALIGN=RIGHT>N/A</TD></TR> | <TD ALIGN=RIGHT>N/A</TD></TR> | ||
<TR> | <TR> | ||
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<TR> | <TR> | ||
<TH>Armadillo dasNov2</TH> | <TH>Armadillo dasNov2</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Microbat myoLuc2</TH> | <TH>Microbat myoLuc2</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>24.363%</TD> | |||
<TD ALIGN=RIGHT>33.650%</TD></TR> | |||
<TR> | |||
<TH>Cow bosTau7</TH> | <TH>Cow bosTau7</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>26.255%</TD> | |||
<TD ALIGN=RIGHT>25.383%</TD></TR> | |||
<TR> | |||
<TH>Sheep oviAri1</TH> | <TH>Sheep oviAri1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>15.341%</TD> | |||
<TD ALIGN=RIGHT>31.925%</TD></TR> | |||
<TR> | |||
<TH>Rock hyrax proCap1</TH> | <TH>Rock hyrax proCap1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Pika ochPri2</TH> | <TH>Pika ochPri2</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Hedgehog eriEur1</TH> | <TH>Hedgehog eriEur1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Tenrec echTel1</TH> | <TH>Tenrec echTel1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Shrew sorAra1</TH> | <TH>Shrew sorAra1</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Wallaby macEug2</TH> | <TH>Wallaby macEug2</TH> | ||
<TD | <TD>no</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
</TR><TR> | <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>in progress</TD><TD ALIGN=RIGHT>in progress</TD> | |||
<TD ALIGN=RIGHT>N/A</TD></TR> | |||
<TR> | |||
<TH>Opossum monDom5</TH> | <TH>Opossum monDom5</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
Revision as of 20:49, 22 March 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 | in progress | 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% |
| 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% |
| 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% |
| Armadillo dasNov2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| 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% |
| Rock hyrax proCap1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Pika ochPri2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Hedgehog eriEur1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Tenrec echTel1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Shrew sorAra1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Wallaby macEug2 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Opossum monDom5 | TBD | |||||||||||||
| Tasmanian devil sarHar1 | TBD | |||||||||||||
| N/A ailMis1 | TBD | |||||||||||||
| N/A croPor1 | TBD | |||||||||||||
| Platypus ornAna1 | TBD | |||||||||||||
| Chicken galGal4 | TBD | |||||||||||||
| Zebra finch taeGut1 | TBD | |||||||||||||
| Turkey melGal1 | TBD | |||||||||||||
| N/A chrPic1 | TBD | |||||||||||||
| Lizard anoCar2 | 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 | |||||||||||||
