Mm10 conservation lastz parameters: Difference between revisions

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(updated data)
(updated data with altered species list)
Line 197: Line 197:
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
  <TH>Manatee&nbsp;triMan1</TH>
  <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
   <TH>Megabat&nbsp;pteVam1</TH>
   <TH>Megabat&nbsp;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 202: Line 205:
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>27.345%</TD>
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>27.345%</TD>
   <TD ALIGN=RIGHT>38.627%</TD></TR>
   <TD ALIGN=RIGHT>38.627%</TD></TR>
<TR>
  <TH>Elephant&nbsp;loxAfr3</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>2012-03-20</TD><TD ALIGN=RIGHT>25.823%</TD>
  <TD ALIGN=RIGHT>21.616%</TD></TR>
<TR>
<TR>
   <TH>Cat&nbsp;felCat4</TH>
   <TH>Cat&nbsp;felCat4</TH>
Line 226: Line 223:
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>29.144%</TD>
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>29.144%</TD>
   <TD ALIGN=RIGHT>31.624%</TD></TR>
   <TD ALIGN=RIGHT>31.624%</TD></TR>
<TR>
  <TH>Elephant&nbsp;loxAfr3</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>2012-03-20</TD><TD ALIGN=RIGHT>25.823%</TD>
  <TD ALIGN=RIGHT>21.616%</TD></TR>
<TR>
<TR>
   <TH>Armadillo&nbsp;dasNov2</TH>
   <TH>Armadillo&nbsp;dasNov2</TH>
Line 251: Line 254:
   <TD ALIGN=RIGHT>31.925%</TD></TR>
   <TD ALIGN=RIGHT>31.925%</TD></TR>
<TR>
<TR>
   <TH>Rock hyrax&nbsp;proCap1</TH>
   <TH>Pika&nbsp;ochPri2</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>
   <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>2012-03-23</TD><TD ALIGN=RIGHT>15.147%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>14.542%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>19.908%</TD></TR>
<TR>
<TR>
   <TH>Pika&nbsp;ochPri2</TH>
   <TH>Rock hyrax&nbsp;proCap1</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>
   <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>2012-03-24</TD><TD ALIGN=RIGHT>in progress</TD>
   <TD>2012-03-23</TD><TD ALIGN=RIGHT>15.147%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>16.214%</TD></TR>
<TR>
<TR>
   <TH>Hedgehog&nbsp;eriEur1</TH>
   <TH>Hedgehog&nbsp;eriEur1</TH>
Line 267: Line 270:
   <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>2012-03-24</TD><TD ALIGN=RIGHT>9.856%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>9.856%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>12.264%</TD></TR>
<TR>
<TR>
   <TH>Tenrec&nbsp;echTel1</TH>
   <TH>Tenrec&nbsp;echTel1</TH>
Line 273: Line 276:
   <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>2012-03-24</TD><TD ALIGN=RIGHT>10.947%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>10.947%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>14.117%</TD></TR>
<TR>
<TR>
   <TH>Shrew&nbsp;sorAra1</TH>
   <TH>Shrew&nbsp;sorAra1</TH>
Line 279: Line 282:
   <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>2012-03-24</TD><TD ALIGN=RIGHT>9.382%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>9.382%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>13.569%</TD></TR>
<TR>
<TR>
   <TH>Wallaby&nbsp;macEug2</TH>
   <TH>Wallaby&nbsp;macEug2</TH>
Line 285: Line 288:
   <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>2012-03-24</TD><TD ALIGN=RIGHT>4.353%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>4.353%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>4.448%</TD></TR>
<TR>
<TR>
   <TH>Opossum&nbsp;monDom5</TH>
   <TH>Opossum&nbsp;monDom5</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Tasmanian devil&nbsp;sarHar1</TH>
   <TH>Tasmanian devil&nbsp;sarHar1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>N/A&nbsp;ailMis1</TH>
   <TH>Budgerigar&nbsp;melUnd1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>N/A&nbsp;croPor1</TH>
   <TH>Platypus&nbsp;ornAna1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Platypus&nbsp;ornAna1</TH>
   <TH>Painted turtle&nbsp;chrPic1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Chicken&nbsp;galGal4</TH>
   <TH>Chicken&nbsp;galGal4</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Zebra finch&nbsp;taeGut1</TH>
   <TH>Zebra finch&nbsp;taeGut1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Lizard&nbsp;anoCar2</TH>
  <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Turkey&nbsp;melGal1</TH>
   <TH>Turkey&nbsp;melGal1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>N/A&nbsp;chrPic1</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
  <TH>Lizard&nbsp;anoCar2</TH>
  <TD COLSPAN=13 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>X. tropicalis&nbsp;xenTro3</TH>
   <TH>X. tropicalis&nbsp;xenTro3</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Coelacanth&nbsp;latCha1</TH>
   <TH>Coelacanth&nbsp;latCha1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Atlantic cod&nbsp;gadMor1</TH>
   <TH>Atlantic cod&nbsp;gadMor1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Nile tilapia&nbsp;oreNil1</TH>
   <TH>Nile tilapia&nbsp;oreNil1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Stickleback&nbsp;gasAcu1</TH>
   <TH>Stickleback&nbsp;gasAcu1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Fugu&nbsp;fr3</TH>
   <TH>Fugu&nbsp;fr3</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Tetraodon&nbsp;tetNig2</TH>
   <TH>Tetraodon&nbsp;tetNig2</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Zebrafish&nbsp;danRer7</TH>
   <TH>Zebrafish&nbsp;danRer7</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TH>Medaka&nbsp;oryLat2</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR><TR>
</TR><TR>
   <TH>Lamprey&nbsp;petMar1</TH>
   <TH>Lamprey&nbsp;petMar1</TH>
   <TD COLSPAN=13 ALIGN=center>TBD</TD>
   <TD COLSPAN=14 ALIGN=center>TBD</TD>
</TR>
</TR>
</TABLE>
</TABLE>

Revision as of 20:34, 29 March 2012

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 mm10
matched
(chainLink table)		 % of query
matched
(chainLinkMm10)
Rat rn4 no045002200human_chimp.v2.q 15000lastz-distrib-1.03.02/bin/lastz15020006002 2012-03-0854.645% 56.348%
Squirrel speTri2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1634.217% 39.244%
Mouse lemur micMur1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1326.636% 37.574%
Kangaroo rat dipOrd1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1619.460% 27.512%
Squirrel monkey saiBol1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0932.339% 33.848%
Naked mole-rat hetGla1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1632.163% 36.427%
Human hg19 yes030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0838.226% 35.249%
Gorilla gorGor3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0833.987% 34.349%
Chimp panTro4 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1034.674% 31.924%
Gibbon nomLeu1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0834.132% 32.372%
Orangutan ponAbe2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0934.496% 30.610%
Tarsier tarSyr1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1224.560% 24.986%
Chinese rhesus rheMac3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0933.931% 33.464%
Baboon papHam1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1033.577% 32.023%
Bushbaby otoGar3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1329.795% 32.926%
Marmoset calJac3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0932.450% 31.301%
Horse equCab2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1634.415% 37.138%
Guinea pig cavPor3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1728.447% 29.115%
Alpaca vicPac1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1722.636% 31.769%
Dolphin turTru1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1728.761% 32.385%
Tree shrew tupBel1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1719.766% 25.144%
Pig susScr2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1723.248% 29.422%
Rabbit oryCun2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1725.248% 25.677%
Sloth choHof1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-22in progress N/A
Manatee triMan1 TBD
Megabat pteVam1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2027.345% 38.627%
Cat felCat4 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2024.033% 30.953%
Panda ailMel1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2030.979% 35.562%
Dog canFam3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2029.144% 31.624%
Elephant loxAfr3 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2025.823% 21.616%
Armadillo dasNov2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2317.004% 19.445%
Microbat myoLuc2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2224.363% 33.650%
Cow bosTau7 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2226.255% 25.383%
Sheep oviAri1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2215.341% 31.925%
Pika ochPri2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2414.542% 19.908%
Rock hyrax proCap1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2315.147% 16.214%
Hedgehog eriEur1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-249.856% 12.264%
Tenrec echTel1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2410.947% 14.117%
Shrew sorAra1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-249.382% 13.569%
Wallaby macEug2 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-244.353% 4.448%
Opossum monDom5 TBD
Tasmanian devil sarHar1 TBD
Budgerigar melUnd1 TBD
Platypus ornAna1 TBD
Painted turtle chrPic1 TBD
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
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