TarSyr2 17-way conservation lastz parameters: Difference between revisions
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</TR> | </TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Bonobo panPan1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>panPan1.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-16</TD><TD ALIGN=RIGHT>52.289%</TD> | ||
<TD ALIGN=RIGHT>59. | <TD ALIGN=RIGHT>59.834%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Chimp panTro4</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>panTro4.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-15</TD><TD ALIGN=RIGHT>51.284%</TD> | ||
<TD ALIGN=RIGHT>56. | <TD ALIGN=RIGHT>56.630%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Orangutan ponAbe2</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>ponAbe2.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-13</TD><TD ALIGN=RIGHT>51.302%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>55.431%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Gorilla gorGor3</TH> | <TH>Gorilla gorGor3</TH> | ||
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<TD>2014-12-13</TD><TD ALIGN=RIGHT>50.262%</TD> | <TD>2014-12-13</TD><TD ALIGN=RIGHT>50.262%</TD> | ||
<TD ALIGN=RIGHT>56.297%</TD></TR> | <TD ALIGN=RIGHT>56.297%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Gibbon nomLeu3</TH> | <TH>Gibbon nomLeu3</TH> | ||
| Line 89: | Line 83: | ||
<TD ALIGN=RIGHT>56.775%</TD></TR> | <TD ALIGN=RIGHT>56.775%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Crab-eating macaque macFas5</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>macFas5.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-16</TD><TD ALIGN=RIGHT>51.814%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>57.176%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Baboon papAnu2</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>papAnu2.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-15</TD><TD ALIGN=RIGHT>51.652%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>56.346%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Rhesus rheMac3</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>rheMac3.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12-16</TD><TD ALIGN=RIGHT> | <TD>2014-12-16</TD><TD ALIGN=RIGHT>50.710%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>59.428%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Green monkey chlSab2</TH> | <TH>Green monkey chlSab2</TH> | ||
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<TD ALIGN=RIGHT>58.191%</TD></TR> | <TD ALIGN=RIGHT>58.191%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Human hg38</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>hg38.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-13</TD><TD ALIGN=RIGHT>52.305%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>56.022%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Golden snub-nosed monkey rhiRox1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>rhiRox1.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12-16</TD><TD ALIGN=RIGHT> | <TD>2014-12-16</TD><TD ALIGN=RIGHT>47.155%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>48.692%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Proboscis monkey nasLar1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>nasLar1.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-16</TD><TD ALIGN=RIGHT>47.164%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>61.165%</TD></TR> | ||
<TR> | <TR> | ||
<TH> | <TH>Squirrel monkey saiBol1</TH> | ||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD> | <TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>saiBol1.tarSyr2.tuning.Q.txt</TD> | ||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | <TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | ||
<TD>2014-12- | <TD>2014-12-15</TD><TD ALIGN=RIGHT>48.208%</TD> | ||
<TD ALIGN=RIGHT> | <TD ALIGN=RIGHT>59.766%</TD></TR> | ||
<TR> | <TR> | ||
<TH>Mouse lemur micMur1</TH> | <TH>Mouse lemur micMur1</TH> | ||
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<TD>2014-12-13</TD><TD ALIGN=RIGHT>38.087%</TD> | <TD>2014-12-13</TD><TD ALIGN=RIGHT>38.087%</TD> | ||
<TD ALIGN=RIGHT>64.649%</TD></TR> | <TD ALIGN=RIGHT>64.649%</TD></TR> | ||
<TR> | |||
<TH>Marmoset calJac3</TH> | |||
<TD>no</TD><TD>50</TD><TD>3000</TD><TD>3000</TD><TD>calJac3.tarSyr2.tuning.Q.txt</TD> | |||
<TD>3400</TD><TD>lastz-distrib-1.03.54/bin/lastz</TD><TD>30</TD><TD>2000</TD><TD>400</TD><TD>2</TD> | |||
<TD>2014-12-13</TD><TD ALIGN=RIGHT>48.629%</TD> | |||
<TD ALIGN=RIGHT>55.800%</TD></TR> | |||
<TR> | <TR> | ||
<TH>Bushbaby otoGar3</TH> | <TH>Bushbaby otoGar3</TH> | ||
Latest revision as of 04:58, 20 December 2014
See Also
- Tarsier 17-way TarSyr2 17-way Genome size statistics
- Tarsier 17-way TarSyr2 17-way conservation alignment
- all other UCSC Multiple Alignments
| The default scoring matrix is: | The HoxD55 scoring matrix is: | The human-chimp.v2 scoring matrix is: | |||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
O=400 E=30 |
O=400 E=30 |
O=600 E=150 |
do not edit, automatically generated table
| query | abridged repeats(no) |
M(0) | K(3000) | L(3000) | Q | Y(9400) | program run | E(30) | H(0) | O(400) | T(1) | chain table date |
% of tarSyr2 matched (chainLink table) |
% of query matched (chainLinkTarSyr2) |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| Bonobo panPan1 | no | 50 | 3000 | 3000 | panPan1.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-16 | 52.289% | 59.834% |
| Chimp panTro4 | no | 50 | 3000 | 3000 | panTro4.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 51.284% | 56.630% |
| Orangutan ponAbe2 | no | 50 | 3000 | 3000 | ponAbe2.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 51.302% | 55.431% |
| Gorilla gorGor3 | no | 50 | 3000 | 3000 | gorGor3.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 50.262% | 56.297% |
| Gibbon nomLeu3 | no | 50 | 3000 | 3000 | nomLeu3.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 50.545% | 56.775% |
| Crab-eating macaque macFas5 | no | 50 | 3000 | 3000 | macFas5.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-16 | 51.814% | 57.176% |
| Baboon papAnu2 | no | 50 | 3000 | 3000 | papAnu2.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 51.652% | 56.346% |
| Rhesus rheMac3 | no | 50 | 3000 | 3000 | rheMac3.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-16 | 50.710% | 59.428% |
| Green monkey chlSab2 | no | 50 | 3000 | 3000 | chlSab2.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-16 | 51.691% | 58.191% |
| Human hg38 | no | 50 | 3000 | 3000 | hg38.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 52.305% | 56.022% |
| Golden snub-nosed monkey rhiRox1 | no | 50 | 3000 | 3000 | rhiRox1.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-16 | 47.155% | 48.692% |
| Proboscis monkey nasLar1 | no | 50 | 3000 | 3000 | nasLar1.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-16 | 47.164% | 61.165% |
| Squirrel monkey saiBol1 | no | 50 | 3000 | 3000 | saiBol1.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 48.208% | 59.766% |
| Mouse lemur micMur1 | no | 50 | 3000 | 3000 | micMur1.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 38.087% | 64.649% |
| Marmoset calJac3 | no | 50 | 3000 | 3000 | calJac3.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-13 | 48.629% | 55.800% |
| Bushbaby otoGar3 | no | 50 | 3000 | 3000 | otoGar3.tarSyr2.tuning.Q.txt | 3400 | lastz-distrib-1.03.54/bin/lastz | 30 | 2000 | 400 | 2 | 2014-12-15 | 44.814% | 59.044% |
