Hg19 conservation lastz parameters: Difference between revisions

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<UL>
<UL>
<LI>[[Hg19 Genome size statistics]]</LI>
<LI>46-way [[Hg19 Genome size statistics]]</LI>
<LI>[[Hg19 conservation alignment]]</LI>
<LI>46-way [[Hg19 conservation alignment]]</LI>
<LI>[[Hg19 Andy's alignment notes]]</LI>
<LI>all other [[UCSC Multiple Alignments]]</LI>
<LI>[[Hg18 44way blastz parameters]]</LI>
<LI>[[Genome size statistics|Hg18 Genome size statistics]]</LI>
<LI>[[Hg18 44way alignment]]</LI>
</UL>
</UL>
<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The human-chimp.v2<BR>scoring matrix is:</TD></TR>
<TR><TD>
<TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-114</TD><TD>-31</TD><TD>-123</TD></TR>
<TR><TH>C</TH><TD>-114</TD><TD>100</TD><TD>-125</TD><TD>-31</TD></TR>
<TR><TH>G</TH><TD>-31</TD><TD>-125</TD><TD>100</TD><TD>-114</TD></TR>
<TR><TH>T</TH><TD>-123</TD><TD>-31</TD><TD>-114</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>91</TD><TD>-90</TD><TD>-25</TD><TD>-100</TD></TR>
<TR><TH>C</TH><TD>-90</TD><TD>100</TD><TD>-100</TD><TD>-25</TD></TR>
<TR><TH>G</TH><TD>-25</TD><TD>-100</TD><TD>100</TD><TD>-90</TD></TR>
<TR><TH>T</TH><TD>-100</TD><TD>-25</TD><TD>-90</TD><TD>91</TD></TR>
</TABLE>
O=400 E=30
</TD><TD WIDTH=42>&nbsp;</TD><TD><TABLE BORDER=1>
<TR><TH>&nbsp;</TH><TH>A</TH><TH>C</TH><TH>G</TH><TH>T</TH></TR>
<TR><TH>A</TH><TD>90</TD><TD>-330</TD><TD>-236</TD><TD>-356</TD></TR>
<TR><TH>C</TH><TD>-330</TD><TD>100</TD><TD>-318</TD><TD>-236</TD></TR>
<TR><TH>G</TH><TD>-236</TD><TD>-318</TD><TD>100</TD><TD>-330</TD></TR>
<TR><TH>T</TH><TD>-356</TD><TD>-236</TD><TD>-330</TD><TD>90</TD></TR>
</TABLE>
O=600 E=150
</TD>
</TR></TABLE>


==do not edit, automatically generated table==
==do not edit, automatically generated table==
Line 96: Line 125:


   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>57.050%</TD>
   <TD ALIGN=RIGHT>66.776%</TD></TR>
   <TD ALIGN=RIGHT>66.774%</TD></TR>
<TR>
<TR>
   <TH>TreeShrew&nbsp;tupBel1</TH>
   <TH>Tree shrew&nbsp;tupBel1</TH>


   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
Line 111: Line 140:
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>


   <TD>2009-06-04</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>48.398%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
Line 118: Line 147:


   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-15</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
Line 125: Line 154:
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-29</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>39.399%</TD>


   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
Line 133: Line 162:
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>


   <TD>2009-05-26</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-05</TD><TD ALIGN=RIGHT>34.377%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
Line 143: Line 172:
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
   <TH>Elephant&nbsp;loxAfr2</TH>
   <TH>Elephant&nbsp;loxAfr3</TH>


   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-28</TD><TD ALIGN=RIGHT>35.153%</TD>
   <TD>2009-07-22</TD><TD ALIGN=RIGHT>46.636%</TD>


   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>42.430%</TD></TR>
<TR>
<TR>
   <TH>Cat&nbsp;felCat3</TH>
   <TH>Cat&nbsp;felCat3</TH>
Line 155: Line 184:
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>


   <TD>2009-05-14</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>35.713%</TD>
   <TD ALIGN=RIGHT>61.135%</TD></TR>
   <TD ALIGN=RIGHT>61.104%</TD></TR>
<TR>
<TR>
   <TH>Dog&nbsp;canFam2</TH>
   <TH>Dog&nbsp;canFam2</TH>
Line 173: Line 202:
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
   <TH>Rabbit&nbsp;oryCun1</TH>
   <TH>Rabbit&nbsp;oryCun2</TH>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>


   <TD>2009-05-29</TD><TD ALIGN=RIGHT>33.676%</TD>
   <TD>2009-08-12</TD><TD ALIGN=RIGHT>44.317%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>48.405%</TD></TR>
<TR>
<TR>
   <TH>Microbat&nbsp;myoLuc1</TH>
   <TH>Microbat&nbsp;myoLuc1</TH>
Line 184: Line 213:


   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-31</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>33.174%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
Line 191: Line 220:
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>no</TD><TD>40M</TD><TD>3000</TD><TD>3000</TD><TD>default</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-04</TD><TD ALIGN=RIGHT>46.506%</TD>


   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>50.297%</TD></TR>
<TR>
<TR>
   <TH>Guinea Pig&nbsp;cavPor3</TH>
   <TH>Guinea Pig&nbsp;cavPor3</TH>
Line 199: Line 228:
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>


   <TD>2009-05-29</TD><TD ALIGN=RIGHT>N/A</TD>
   <TD>2009-06-06</TD><TD ALIGN=RIGHT>43.680%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>N/A</TD></TR>
<TR>
<TR>
Line 273: Line 302:
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
   <TD>2009-05-29</TD><TD ALIGN=RIGHT>14.358%</TD>
   <TD ALIGN=RIGHT>N/A</TD></TR>
   <TD ALIGN=RIGHT>11.615%</TD></TR>
<TR>
<TR>
   <TH>Platypus&nbsp;ornAna1</TH>
   <TH>Platypus&nbsp;ornAna1</TH>
Line 327: Line 356:
   <TD ALIGN=RIGHT>10.929%</TD></TR>
   <TD ALIGN=RIGHT>10.929%</TD></TR>
<TR>
<TR>
   <TH>Zebrafish&nbsp;danRer5</TH>
   <TH>Zebrafish&nbsp;danRer6</TH>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>no</TD><TD>40M</TD><TD>2200</TD><TD>6000</TD><TD>HoxD55.q</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>


   <TD>2009-05-26</TD><TD ALIGN=RIGHT>2.562%</TD>
   <TD>2009-07-10</TD><TD ALIGN=RIGHT>3.051%</TD>
   <TD ALIGN=RIGHT>5.144%</TD></TR>
   <TD ALIGN=RIGHT>6.399%</TD></TR>
<TR>
<TR>
   <TH>Tetraodon&nbsp;tetNig1</TH>
   <TH>Tetraodon&nbsp;tetNig2</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>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-14</TD><TD ALIGN=RIGHT>2.003%</TD>
   <TD>2009-08-10</TD><TD ALIGN=RIGHT>1.712%</TD>
   <TD ALIGN=RIGHT>14.443%</TD></TR>
   <TD ALIGN=RIGHT>14.194%</TD></TR>
<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>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-22</TD><TD ALIGN=RIGHT>1.849%</TD>
   <TD>2009-05-22</TD><TD ALIGN=RIGHT>1.849%</TD>
   <TD ALIGN=RIGHT>6.705%</TD></TR>
   <TD ALIGN=RIGHT>6.705%</TD></TR>
<TR>
<TR>
Line 352: Line 378:
   <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>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>3400</TD><TD>lastz</TD><TD>30</TD><TD>0</TD><TD>400</TD><TD>1</TD>
   <TD>2009-05-14</TD><TD ALIGN=RIGHT>1.082%</TD>
   <TD>2009-05-14</TD><TD ALIGN=RIGHT>1.082%</TD>
   <TD ALIGN=RIGHT>3.200%</TD></TR>
   <TD ALIGN=RIGHT>3.200%</TD></TR>
</TABLE>
</TABLE>


[[Category:Comparative Genomics]]
[[Category:Comparative Genomics]]

Latest revision as of 22:29, 18 May 2011

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(40M)K(3000) L(3000)QY(9400) program
run		E(30)H(0) O(400)T(1) chain table
date		 % of hg19
matched
(chainLink table)		 % of query
matched
(chainLinkHg19)
Chimp panTro2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-03-2094.846% 94.908%
Gorilla gorGor1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-03-2259.484% N/A
Orangutan ponAbe2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-1491.350% 89.617%
Rhesus rheMac2 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-1482.744% 87.422%
Baboon papHam1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-2082.810% N/A
Marmoset calJac1 no25445003000human_chimp.v2.q 15000lastz15006002 2009-05-1470.860% 71.897%
Tarsier tarSyr1 no40M30003000default 9400lastz3004001 2009-05-1547.830% N/A
Mouse lemur micMur1 no40M30003000default 9400lastz3004001 2009-05-2246.519% N/A
Bushbaby otoGar1 no40M30003000default 9400lastz3004001 2009-05-1543.644% N/A
Horse equCab2 no40M30003000default 9400lastz3004001 2009-06-0457.050% 66.774%
Tree shrew tupBel1 no40M30003000default 9400lastz3004001 2009-06-0136.156% N/A
Dolphin turTru1 no40M30003000default 9400lastz3004001 2009-06-0448.398% N/A
Squirrel speTri1 no40M30003000default 9400lastz3004001 2009-06-0435.713% N/A
Alpaca vicPac1 no40M30003000default 9400lastz3004001 2009-06-0439.399% N/A
Sloth choHof1 no40M30003000default 9400lastz3004001 2009-06-0534.377% N/A
Megabat pteVam1 no40M30003000default 9400lastz3004001 2009-06-0445.414% N/A
Elephant loxAfr3 no5030003000default 9400lastz3004001 2009-07-2246.636% 42.430%
Cat felCat3 no40M30003000default 9400lastz3004001 2009-06-0435.713% 61.104%
Dog canFam2 yes40M30003000default 9400lastz3004001 2009-05-1452.879% 62.055%
Armadillo dasNov2 no5030003000default 9400lastz3004001 2009-05-2733.543% N/A
Rabbit oryCun2 no5030003000default 9400lastz3004001 2009-08-1244.317% 48.405%
Microbat myoLuc1 no40M30003000default 9400lastz3004001 2009-06-0433.174% N/A
Cow bosTau4 no40M30003000default 9400lastz3004001 2009-06-0446.506% 50.297%
Guinea Pig cavPor3 no40M30003000default 9400lastz3004001 2009-06-0643.680% N/A
Rock hyrax proCap1 no5030003000default 9400lastz3004001 2009-05-2630.864% N/A
Kangaroo rat dipOrd1 no5030003000default 9400lastz3004001 2009-05-2927.161% N/A
Pika ochPri2 no5030003000default 9400lastz3004001 2009-05-3027.768% N/A
Hedgehog eriEur1 no5030003000default 9400lastz3004001 2009-05-3019.362% N/A
Tenrec echTel1 no5030003000default 9400lastz3004001 2009-05-2823.120% N/A
Mouse mm9 yes40M30003000default 9400lastz3004001 2009-05-1335.299% 38.693%
Rat rn4 yes40M30003000default 9400lastz3004001 2009-05-1332.879% 36.860%
Shrew sorAra1 no5030003000default 9400lastz3004001 2009-05-2919.760% N/A
Wallaby macEug1 no5030003000default 9400lastz3004001 2009-05-316.011% N/A
Opossum monDom5 no5022006000HoxD55.q 3400lastz3004001 2009-05-2914.358% 11.615%
Platypus ornAna1 no40M22006000HoxD55.q 3400lastz3020004001 2009-05-277.627% 11.259%
Chicken galGal3 yes40M220010000HoxD55.q 3400lastz3020004001 2009-05-143.591% 8.786%
Zebra finch taeGut1 no40M220010000HoxD55.q 3400lastz3020004001 2009-05-263.496% 7.795%
Lizard anoCar1 no40M22006000HoxD55.q 3400lastz3020004001 2009-05-303.591% 5.146%
X. tropicalis xenTro2 no40M22006000HoxD55.q 3400lastz3020004001 2009-05-273.176% 6.773%
Stickleback gasAcu1 no5022006000HoxD55.q 3400lastz3004001 2009-05-141.916% 11.175%
Fugu fr2 no5022006000HoxD55.q 3400lastz3004001 2009-05-201.702% 10.929%
Zebrafish danRer6 no40M22006000HoxD55.q 3400lastz3020004001 2009-07-103.051% 6.399%
Tetraodon tetNig2 no5022006000HoxD55.q 3400lastz3004001 2009-08-101.712% 14.194%
Medaka oryLat2 no5022006000HoxD55.q 3400lastz3004001 2009-05-221.849% 6.705%
Lamprey petMar1 no5022006000HoxD55.q 3400lastz3004001 2009-05-141.082% 3.200%
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