Ce11 26-way conservation lastz parameters: Difference between revisions

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   <TD ALIGN=RIGHT>3.405%</TD></TR>
   <TD ALIGN=RIGHT>3.405%</TD></TR>
<TR>
<TR>
   <TH>Hookworm&nbsp;ancCey1</TH>
   <TH>A. ceylanicum&nbsp;ancCey1</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-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>3.237%</TD></TR>
   <TD ALIGN=RIGHT>3.237%</TD></TR>
<TR>
<TR>
   <TH>Hookworm&nbsp;necAme1</TH>
   <TH>N. americanus&nbsp;necAme1</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-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <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-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2015-07-08</TD><TD ALIGN=RIGHT>5.052%</TD>
   <TD>2015-08-11</TD><TD ALIGN=RIGHT>5.065%</TD>
   <TD ALIGN=RIGHT>5.532%</TD></TR>
   <TD ALIGN=RIGHT>5.521%</TD></TR>
<TR>
<TR>
   <TH>Root knot&nbsp;melHap1</TH>
   <TH>M. hapla&nbsp;melHap1</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-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
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   <TD ALIGN=RIGHT>6.840%</TD></TR>
   <TD ALIGN=RIGHT>6.840%</TD></TR>
<TR>
<TR>
   <TH>Root knot&nbsp;melInc2</TH>
   <TH>M. incognita&nbsp;melInc2</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-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
Line 176: Line 176:
   <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-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>9400</TD><TD>lastz-distrib-1.03.66/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>1</TD>
   <TD>2015-07-09</TD><TD ALIGN=RIGHT>5.182%</TD>
   <TD>2015-08-10</TD><TD ALIGN=RIGHT>5.193%</TD>
   <TD ALIGN=RIGHT>5.093%</TD></TR>
   <TD ALIGN=RIGHT>5.092%</TD></TR>
<TR>
<TR>
   <TH>Trichinella&nbsp;triSpi1</TH>
   <TH>Trichinella&nbsp;triSpi1</TH>

Revision as of 20:35, 27 August 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 ce11
matched
(chainLink table)		 % of query
matched
(chainLinkCe11)
C. japonica caeJap4 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-06-2527.709% 19.533%
C. brenneri caePb3 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-0140.638% 32.296%
C. remanei caeRem4 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-0241.715% 33.416%
C. tropicalis caeSp111 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-0737.870% 47.362%
C. briggsae cb4 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-0139.384% 36.204%
C. angaria caeAng2 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-06-3017.682% 20.987%
C. sp. 5 ju800 caeSp51 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-0940.332% 31.721%
H. bacteriophora/m31e hetBac1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-2310.486% 13.556%
Microworm panRed1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-016.585% 10.359%
Threadworm strRat2 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-095.669% 11.848%
Pig roundworm ascSuu1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-235.722% 2.224%
Barber pole worm haeCon2 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-078.936% 3.405%
A. ceylanicum ancCey1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-239.736% 3.237%
N. americanus necAme1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-238.902% 4.115%
P. exspectatus priExs1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-236.222% 4.321%
P. pacificus priPac3 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-016.308% 4.534%
Pine wood nematode burXyl1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-096.291% 8.293%
Filarial worm bruMal2 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-08-115.065% 5.521%
M. hapla melHap1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-06-263.916% 6.840%
M. incognita melInc2 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-06-303.516% 5.539%
O. volvulus oncVol1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-08-105.193% 5.092%
Trichinella triSpi1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-232.848% 4.678%
Whipworm triSui1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-232.917% 3.714%
Dog heartworm dirImm1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-235.005% 5.474%
Eye worm loaLoa1 no5030003000default 9400lastz-distrib-1.03.66/bin/lastz3020004001 2015-07-235.056% 5.274%
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