GeoFor1 conservation lastz parameters: Difference between revisions

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(better order)
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   <TD>2012-07-31</TD><TD ALIGN=RIGHT>92.532%</TD>
   <TD>2012-07-31</TD><TD ALIGN=RIGHT>92.532%</TD>
   <TD ALIGN=RIGHT>92.089%</TD></TR>
   <TD ALIGN=RIGHT>92.089%</TD></TR>
<TR>
  <TH>Budgerigar&nbsp;melUnd1</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>2012-07-29</TD><TD ALIGN=RIGHT>80.650%</TD>
  <TD ALIGN=RIGHT>76.598%</TD></TR>
<TR>
<TR>
   <TH>Chicken&nbsp;galGal4</TH>
   <TH>Chicken&nbsp;galGal4</TH>
Line 70: Line 76:
   <TD>2012-07-29</TD><TD ALIGN=RIGHT>67.079%</TD>
   <TD>2012-07-29</TD><TD ALIGN=RIGHT>67.079%</TD>
   <TD ALIGN=RIGHT>72.625%</TD></TR>
   <TD ALIGN=RIGHT>72.625%</TD></TR>
<TR>
  <TH>Budgerigar&nbsp;melUnd1</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>2012-07-29</TD><TD ALIGN=RIGHT>80.650%</TD>
  <TD ALIGN=RIGHT>76.598%</TD></TR>
<TR>
<TR>
   <TH>Human&nbsp;hg19</TH>
   <TH>Human&nbsp;hg19</TH>

Revision as of 23:29, 2 August 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 geoFor1
matched
(chainLink table)
% of query
matched
(chainLinkGeoFor1)
Zebra finch taeGut1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-3192.532% 92.089%
Budgerigar melUnd1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-2980.650% 76.598%
Chicken galGal4 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-3070.718% 72.077%
Turkey melGal1 no030002200default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-2967.079% 72.625%
Human hg19 no0220010000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-298.504% 3.503%
Mouse mm10 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-07-297.709% 3.543%