Hg38 100-way conservation lastz parameters: Difference between revisions

From genomewiki
Jump to navigationJump to search
(starting hg38 100 way)
 
(updated)
Line 285: Line 285:
</TR><TR>
</TR><TR>
   <TH>Green seaturtle&nbsp;cheMyd1</TH>
   <TH>Green seaturtle&nbsp;cheMyd1</TH>
   <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>hg38.cheMyd1.tuning.Q.txt</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2015-02-05</TD><TD ALIGN=RIGHT>2.457%</TD>
   <TD>2015-02-06</TD><TD ALIGN=RIGHT>6.296%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>7.960%</TD></TR>
<TR>
<TR>
   <TH>Painted turtle&nbsp;chrPic2</TH>
   <TH>Painted turtle&nbsp;chrPic2</TH>
   <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>hg38.chrPic2.tuning.Q.txt</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2015-02-05</TD><TD ALIGN=RIGHT>2.482%</TD>
   <TD>2015-02-06</TD><TD ALIGN=RIGHT>6.708%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>8.554%</TD></TR>
<TR>
<TR>
   <TH>Chinese softshell turtle&nbsp;pelSin1</TH>
   <TH>Chinese softshell turtle&nbsp;pelSin1</TH>
Line 312: Line 312:
</TR><TR>
</TR><TR>
   <TH>Lizard&nbsp;anoCar2</TH>
   <TH>Lizard&nbsp;anoCar2</TH>
   <TD>no</TD><TD>254</TD><TD>3000</TD><TD>3000</TD><TD>hg38.anoCar2.tuning.Q.txt</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2015-02-05</TD><TD ALIGN=RIGHT>1.464%</TD>
   <TD>2015-02-06</TD><TD ALIGN=RIGHT>3.593%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>5.222%</TD></TR>
<TR>
<TR>
   <TH>Mallard duck&nbsp;anaPla1</TH>
   <TH>Mallard duck&nbsp;anaPla1</TH>
Line 390: Line 390:
</TR><TR>
</TR><TR>
   <TH>Lamprey&nbsp;petMar2</TH>
   <TH>Lamprey&nbsp;petMar2</TH>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
</TR><TR>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TH>Zebrafish&nbsp;danRer7</TH>
  <TD>2015-02-06</TD><TD ALIGN=RIGHT>1.265%</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
  <TD ALIGN=RIGHT>3.960%</TD></TR>
</TR><TR>
<TR>
   <TH>Zebrafish&nbsp;danRer10</TH>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-02-08</TD><TD ALIGN=RIGHT>3.357%</TD>
  <TD ALIGN=RIGHT>7.110%</TD></TR>
<TR>
   <TH>Zebra Mbuna&nbsp;mayZeb1</TH>
   <TH>Zebra Mbuna&nbsp;mayZeb1</TH>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
</TR><TR>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-02-07</TD><TD ALIGN=RIGHT>1.805%</TD>
  <TD ALIGN=RIGHT>6.780%</TD></TR>
<TR>
   <TH>Pundamilia nyererei&nbsp;punNye1</TH>
   <TH>Pundamilia nyererei&nbsp;punNye1</TH>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
</TR><TR>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-02-06</TD><TD ALIGN=RIGHT>1.787%</TD>
  <TD ALIGN=RIGHT>6.864%</TD></TR>
<TR>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
Line 408: Line 420:
<TR>
<TR>
   <TH>Southern platyfish&nbsp;xipMac1</TH>
   <TH>Southern platyfish&nbsp;xipMac1</TH>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
   <TD>no</TD><TD>50</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
</TR>
  <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
  <TD>2015-02-06</TD><TD ALIGN=RIGHT>1.898%</TD>
  <TD ALIGN=RIGHT>7.435%</TD></TR>
</TABLE>
</TABLE>

Revision as of 19:44, 10 February 2015

See Also


The default
scoring matrix is:		  The HoxD55
scoring matrix is:		 The human-chimp.v2
scoring matrix is:
 ACGT
A91-114-31-123
C-114100-125-31
G-31-125100-114
T-123-31-11491

O=400 E=30

 
 ACGT
A91-90-25-100
C-90100-100-25
G-25-100100-90
T-100-25-9091

O=400 E=30

 
 ACGT
A90-330-236-356
C-330100-318-236
G-236-318100-330
T-356-236-33090

O=600 E=150

do not edit, automatically generated table

query abridged
repeats(no)		 M(0)K(3000) L(3000)QY(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 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-05-2793.112% 95.664%
Gorilla gorGor3 no25430003000hg38.gorGor3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1588.005% 91.695%
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-09-0289.187% 89.656%
Gibbon nomLeu3 no25430003000hg38.nomLeu3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1286.379% 90.470%
Crab-eating macaque macFas5 no25430003000hg38.macFas5.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1485.675% 87.749%
Rhesus rheMac3 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-01-2879.729% 86.715%
Baboon papAnu2 no25430003000hg38.papAnu2.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1384.179% 84.502%
Squirrel monkey saiBol1 no25430003000hg38.saiBol1.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1370.565% 81.466%
Green monkey chlSab2 no25445003000human_chimp.v2.q 15000lastz-distrib-1.03.52/bin/lastz15020006002 2014-07-1184.393% 88.264%
Marmoset calJac3 no25430003000hg38.calJac3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1371.709% 76.757%
Aardvark oryAfe1 TBD
Bushbaby otoGar3 no25430003000hg38.otoGar3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004002 2014-12-1349.485% 60.561%
White rhinoceros cerSim1 TBD
Cape golden mole chrAsi1 TBD
Big brown bat eptFus1 TBD
Chinese tree shrew tupChi1 TBD
Horse equCab2 TBD
Bactrian camel camFer1 TBD
Alpaca vicPac2 TBD
Dolphin turTru2 TBD
Dog canFam3 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-01-2749.978% 60.083%
Killer whale orcOrc1 TBD
Squirrel speTri2 TBD
Black flying-fox pteAle1 TBD
Pig susScr3 TBD
Elephant loxAfr3 TBD
Naked mole-rat hetGla2 TBD
Megabat pteVam1 TBD
Cat felCat8 TBD
Panda ailMel1 TBD
Ferret  musFur1 TBD
Guinea pig cavPor3 TBD
Armadillo dasNov3 TBD
Rabbit oryCun2 TBD
Tibetan antelope panHod1 TBD
Weddell seal lepWed1 TBD
Pacific walrus odoRosDiv1 TBD
David's myotis (bat) myoDav1 TBD
Cow bosTau8 no25430003000default 9400lastz3020004001 2014-10-1645.975% 50.440%
Domestic goat capHir1 TBD
Sheep oviAri3 no25430003000hg38.oviAri3.tuning.Q.txt 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-01-2141.193% 47.075%
Microbat myoLuc2 TBD
Cape elephant shrew eleEdw1 TBD
Manatee triMan1 TBD
Lesser Egyptian jerboa jacJac1 TBD
Chinchilla chiLan1 TBD
Star-nosed mole conCri1 TBD
Brush-tailed rat octDeg1 TBD
Pika ochPri3 TBD
Hedgehog eriEur2 TBD
Tenrec echTel2 TBD
Mouse mm10 no030003000default 9400lastz-distrib-1.03.52/bin/lastz3020004001 2014-01-2531.629% 35.323%
Rat rn6 TBD
Chinese hamster criGri1 TBD
Golden hamster mesAur1 TBD
Prairie vole micOch1 TBD
Shrew sorAra2 TBD
Wallaby macEug2 TBD
Opossum monDom5 no5022006000HoxD55.q 3400lastz-distrib-1.03.52/bin/lastz3020004001 2014-05-2914.370% 11.996%
Tasmanian devil sarHar1 TBD
Spiny softshell turtle apaSpi1 TBD
Green seaturtle cheMyd1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-066.296% 7.960%
Painted turtle chrPic2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-066.708% 8.554%
Chinese softshell turtle pelSin1 TBD
Platypus ornAna1 TBD
American alligator allMis1 TBD
Rock pigeon colLiv1 TBD
Chicken galGal4 TBD
Lizard anoCar2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-063.593% 5.222%
Mallard duck anaPla1 TBD
Turkey melGal1 TBD
Saker falcon falChe1 TBD
Peregrine falcon falPer1 TBD
Parrot amaVit1 TBD
Scarlet Macaw araMac1 TBD
Tibetan ground jay pseHum1 TBD
Budgerigar melUnd1 TBD
Collared flycatcher ficAlb2 TBD
White-throated sparrow zonAlb1 TBD
Medium ground finch geoFor1 TBD
Zebra finch taeGut2 TBD
Spotted gar lepOcu1 TBD
X. tropicalis xenTro7 TBD
Coelacanth latCha1 TBD
Atlantic cod gadMor1 TBD
Stickleback gasAcu1 TBD
Nile tilapia oreNil2 TBD
Tetraodon tetNig2 TBD
Princess of Burundi neoBri1 TBD
Yellowbelly pufferfish takFla1 TBD
Burton's mouthbreeder hapBur1 TBD
Fugu fr3 TBD
Mexican tetra (cavefish) astMex1 TBD
Lamprey petMar2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.265% 3.960%
Zebrafish danRer10 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-083.357% 7.110%
Zebra Mbuna mayZeb1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-071.805% 6.780%
Pundamilia nyererei punNye1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.787% 6.864%
Medaka oryLat2 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-062.002% 6.853%
Southern platyfish xipMac1 no5022006000HoxD55.q 3400lastz-distrib-1.03.54/bin/lastz3020004001 2015-02-061.898% 7.435%
Retrieved from "https://genomewiki.ucsc.edu/index.php?title=Hg38_100-way_conservation_lastz_parameters&oldid=22414"