Mm10 conservation lastz parameters: Difference between revisions
From genomewiki
Jump to navigationJump to search
(initial contents) |
(update information) |
||
| Line 60: | Line 60: | ||
<TR> | <TR> | ||
<TH>Squirrel speTri2</TH> | <TH>Squirrel speTri2</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>2012-03-16</TD><TD ALIGN=RIGHT>34.217%</TD> | |||
<TD ALIGN=RIGHT>39.244%</TD></TR> | |||
<TR> | |||
<TH>Mouse lemur micMur1</TH> | <TH>Mouse lemur micMur1</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 69: | Line 72: | ||
<TR> | <TR> | ||
<TH>Kangaroo rat dipOrd1</TH> | <TH>Kangaroo rat dipOrd1</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>2012-03-16</TD><TD ALIGN=RIGHT>19.460%</TD> | |||
<TD ALIGN=RIGHT>27.512%</TD></TR> | |||
<TR> | |||
<TH>Squirrel monkey saiBol1</TH> | <TH>Squirrel monkey saiBol1</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 78: | Line 84: | ||
<TR> | <TR> | ||
<TH>Naked mole-rat hetGla1</TH> | <TH>Naked mole-rat hetGla1</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>2012-03-16</TD><TD ALIGN=RIGHT>32.163%</TD> | |||
<TD ALIGN=RIGHT>36.427%</TD></TR> | |||
<TR> | |||
<TH>Human hg19</TH> | <TH>Human hg19</TH> | ||
<TD>yes</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | <TD>yes</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD> | ||
| Line 141: | Line 150: | ||
<TR> | <TR> | ||
<TH>Horse equCab2</TH> | <TH>Horse equCab2</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>Guinea pig cavPor3</TH> | <TH>Guinea pig cavPor3</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>Alpaca vicPac1</TH> | <TH>Alpaca vicPac1</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>Dolphin turTru1</TH> | <TH>Dolphin turTru1</TH> | ||
<TD COLSPAN=13 ALIGN=center>TBD</TD> | <TD COLSPAN=13 ALIGN=center>TBD</TD> | ||
Revision as of 22:39, 16 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 | in progress | in progress | N/A |
| Guinea pig cavPor3 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Alpaca vicPac1 | no | 0 | 3000 | 2200 | default | 9400 | lastz-distrib-1.03.02/bin/lastz | 30 | 2000 | 400 | 1 | in progress | in progress | N/A |
| Dolphin turTru1 | TBD | |||||||||||||
| Tree shrew tupBel1 | TBD | |||||||||||||
| Pig susScr2 | TBD | |||||||||||||
| Rabbit oryCun2 | TBD | |||||||||||||
| Sloth choHof1 | TBD | |||||||||||||
| Megabat pteVam1 | TBD | |||||||||||||
| Elephant loxAfr3 | TBD | |||||||||||||
| Cat felCat4 | TBD | |||||||||||||
| Panda ailMel1 | TBD | |||||||||||||
| Dog canFam3 | TBD | |||||||||||||
| Armadillo dasNov2 | TBD | |||||||||||||
| Microbat myoLuc2 | TBD | |||||||||||||
| Cow bosTau7 | TBD | |||||||||||||
| Sheep oviAri1 | TBD | |||||||||||||
| Rock hyrax proCap1 | TBD | |||||||||||||
| Pika ochPri2 | TBD | |||||||||||||
| Hedgehog eriEur1 | TBD | |||||||||||||
| Tenrec echTel1 | TBD | |||||||||||||
| Shrew sorAra1 | TBD | |||||||||||||
| Wallaby macEug2 | TBD | |||||||||||||
| 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 | |||||||||||||
