Mm10 conservation lastz parameters: Difference between revisions

From genomewiki
Jump to navigationJump to search
(updated with new genomes)
(fixup default L value)
 
(One intermediate revision by the same user not shown)
Line 10: Line 10:
<TABLE BORDER=0>
<TABLE BORDER=0>
<TR><TD>The default<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD>
<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>
<TD>The HoxD55<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The human-chimp.v2<BR>scoring matrix is:</TD><TD WIDTH=42>&nbsp;</TD><TD>The mouse_rat_2.q<BR>scoring matrix is:</TD></TR>


<TR><TD>
<TR><TD>
Line 37: Line 37:
</TABLE>
</TABLE>
O=600 E=150
O=600 E=150
</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>100</TD><TD>-139</TD><TD>-54</TD><TD>-170</TD></TR>
<TR><TH>C</TH><TD>-139</TD><TD>95</TD><TD>-83</TD><TD>-54</TD></TR>
<TR><TH>G</TH><TD>-54</TD><TD>-83</TD><TD>95</TD><TD>-139</TD></TR>
<TR><TH>T</TH><TD>-170</TD><TD>-54</TD><TD>-139</TD><TD>100</TD></TR>
</TABLE>
O=600 E=55
</TD>
</TD>
</TR></TABLE>
</TR></TABLE>
Line 60: Line 68:
<TR>
<TR>
   <TH>Squirrel&nbsp;speTri2</TH>
   <TH>Squirrel&nbsp;speTri2</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>3000</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>2012-03-16</TD><TD ALIGN=RIGHT>34.217%</TD>
   <TD>2012-03-16</TD><TD ALIGN=RIGHT>34.217%</TD>
Line 66: Line 74:
<TR>
<TR>
   <TH>Kangaroo rat&nbsp;dipOrd1</TH>
   <TH>Kangaroo rat&nbsp;dipOrd1</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>3000</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>2012-03-16</TD><TD ALIGN=RIGHT>19.460%</TD>
   <TD>2012-03-16</TD><TD ALIGN=RIGHT>19.460%</TD>
Line 72: Line 80:
<TR>
<TR>
   <TH>Naked mole rat&nbsp;hetGla2</TH>
   <TH>Naked mole rat&nbsp;hetGla2</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>3000</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>2012-04-14</TD><TD ALIGN=RIGHT>32.753%</TD>
   <TD>2012-04-14</TD><TD ALIGN=RIGHT>32.753%</TD>
Line 78: Line 86:
<TR>
<TR>
   <TH>Guinea pig&nbsp;cavPor3</TH>
   <TH>Guinea pig&nbsp;cavPor3</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>3000</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>2012-03-17</TD><TD ALIGN=RIGHT>28.447%</TD>
   <TD>2012-03-17</TD><TD ALIGN=RIGHT>28.447%</TD>
Line 84: Line 92:
<TR>
<TR>
   <TH>Rabbit&nbsp;oryCun2</TH>
   <TH>Rabbit&nbsp;oryCun2</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>3000</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>2012-03-17</TD><TD ALIGN=RIGHT>25.248%</TD>
   <TD>2012-03-17</TD><TD ALIGN=RIGHT>25.248%</TD>
Line 90: Line 98:
<TR>
<TR>
   <TH>Pika&nbsp;ochPri2</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>3000</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>14.542%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>14.542%</TD>
Line 96: Line 104:
<TR>
<TR>
   <TH>Tree shrew&nbsp;tupBel1</TH>
   <TH>Tree shrew&nbsp;tupBel1</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>3000</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>2012-03-17</TD><TD ALIGN=RIGHT>19.766%</TD>
   <TD>2012-03-17</TD><TD ALIGN=RIGHT>19.766%</TD>
Line 102: Line 110:
<TR>
<TR>
   <TH>Human&nbsp;hg19</TH>
   <TH>Human&nbsp;hg19</TH>
   <TD>yes</TD><TD>0</TD><TD>3000</TD><TD>2200</TD><TD>default</TD>
   <TD>yes</TD><TD>0</TD><TD>3000</TD><TD>3000</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>2012-03-08</TD><TD ALIGN=RIGHT>38.226%</TD>
   <TD>2012-03-08</TD><TD ALIGN=RIGHT>38.226%</TD>
Line 108: Line 116:
<TR>
<TR>
   <TH>Gorilla&nbsp;gorGor3</TH>
   <TH>Gorilla&nbsp;gorGor3</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>3000</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>2012-03-08</TD><TD ALIGN=RIGHT>33.987%</TD>
   <TD>2012-03-08</TD><TD ALIGN=RIGHT>33.987%</TD>
Line 114: Line 122:
<TR>
<TR>
   <TH>Chimp&nbsp;panTro4</TH>
   <TH>Chimp&nbsp;panTro4</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>3000</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>2012-03-10</TD><TD ALIGN=RIGHT>34.674%</TD>
   <TD>2012-03-10</TD><TD ALIGN=RIGHT>34.674%</TD>
Line 120: Line 128:
<TR>
<TR>
   <TH>Gibbon&nbsp;nomLeu2</TH>
   <TH>Gibbon&nbsp;nomLeu2</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>3000</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>2012-04-14</TD><TD ALIGN=RIGHT>34.031%</TD>
   <TD>2012-04-14</TD><TD ALIGN=RIGHT>34.031%</TD>
Line 126: Line 134:
<TR>
<TR>
   <TH>Orangutan&nbsp;ponAbe2</TH>
   <TH>Orangutan&nbsp;ponAbe2</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>3000</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>2012-03-09</TD><TD ALIGN=RIGHT>34.496%</TD>
   <TD>2012-03-09</TD><TD ALIGN=RIGHT>34.496%</TD>
Line 132: Line 140:
<TR>
<TR>
   <TH>Tarsier&nbsp;tarSyr1</TH>
   <TH>Tarsier&nbsp;tarSyr1</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>3000</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>2012-03-12</TD><TD ALIGN=RIGHT>24.560%</TD>
   <TD>2012-03-12</TD><TD ALIGN=RIGHT>24.560%</TD>
Line 138: Line 146:
<TR>
<TR>
   <TH>Chinese rhesus&nbsp;rheMac3</TH>
   <TH>Chinese rhesus&nbsp;rheMac3</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>3000</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>2012-03-09</TD><TD ALIGN=RIGHT>33.931%</TD>
   <TD>2012-03-09</TD><TD ALIGN=RIGHT>33.931%</TD>
Line 144: Line 152:
<TR>
<TR>
   <TH>Baboon&nbsp;papHam1</TH>
   <TH>Baboon&nbsp;papHam1</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>3000</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>2012-03-10</TD><TD ALIGN=RIGHT>33.577%</TD>
   <TD>2012-03-10</TD><TD ALIGN=RIGHT>33.577%</TD>
Line 150: Line 158:
<TR>
<TR>
   <TH>Bushbaby&nbsp;otoGar3</TH>
   <TH>Bushbaby&nbsp;otoGar3</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>3000</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>2012-03-13</TD><TD ALIGN=RIGHT>29.795%</TD>
   <TD>2012-03-13</TD><TD ALIGN=RIGHT>29.795%</TD>
Line 156: Line 164:
<TR>
<TR>
   <TH>Marmoset&nbsp;calJac3</TH>
   <TH>Marmoset&nbsp;calJac3</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>3000</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>2012-03-09</TD><TD ALIGN=RIGHT>32.450%</TD>
   <TD>2012-03-09</TD><TD ALIGN=RIGHT>32.450%</TD>
Line 162: Line 170:
<TR>
<TR>
   <TH>Mouse lemur&nbsp;micMur1</TH>
   <TH>Mouse lemur&nbsp;micMur1</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>3000</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>2012-03-13</TD><TD ALIGN=RIGHT>26.636%</TD>
   <TD>2012-03-13</TD><TD ALIGN=RIGHT>26.636%</TD>
Line 168: Line 176:
<TR>
<TR>
   <TH>Squirrel monkey&nbsp;saiBol1</TH>
   <TH>Squirrel monkey&nbsp;saiBol1</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>3000</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>2012-03-09</TD><TD ALIGN=RIGHT>32.339%</TD>
   <TD>2012-03-09</TD><TD ALIGN=RIGHT>32.339%</TD>
Line 174: Line 182:
<TR>
<TR>
   <TH>Horse&nbsp;equCab2</TH>
   <TH>Horse&nbsp;equCab2</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>3000</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>2012-03-16</TD><TD ALIGN=RIGHT>34.415%</TD>
   <TD>2012-03-16</TD><TD ALIGN=RIGHT>34.415%</TD>
Line 180: Line 188:
<TR>
<TR>
   <TH>Alpaca&nbsp;vicPac1</TH>
   <TH>Alpaca&nbsp;vicPac1</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>3000</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>2012-03-17</TD><TD ALIGN=RIGHT>22.636%</TD>
   <TD>2012-03-17</TD><TD ALIGN=RIGHT>22.636%</TD>
Line 186: Line 194:
<TR>
<TR>
   <TH>Dolphin&nbsp;turTru2</TH>
   <TH>Dolphin&nbsp;turTru2</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>3000</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>2012-04-14</TD><TD ALIGN=RIGHT>30.267%</TD>
   <TD>2012-04-14</TD><TD ALIGN=RIGHT>30.267%</TD>
Line 192: Line 200:
<TR>
<TR>
   <TH>Pig&nbsp;susScr3</TH>
   <TH>Pig&nbsp;susScr3</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>3000</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>2012-04-14</TD><TD ALIGN=RIGHT>25.685%</TD>
   <TD>2012-04-14</TD><TD ALIGN=RIGHT>25.685%</TD>
Line 198: Line 206:
<TR>
<TR>
   <TH>Cow&nbsp;bosTau7</TH>
   <TH>Cow&nbsp;bosTau7</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>3000</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>2012-03-22</TD><TD ALIGN=RIGHT>26.255%</TD>
   <TD>2012-03-22</TD><TD ALIGN=RIGHT>26.255%</TD>
Line 204: Line 212:
<TR>
<TR>
   <TH>Sheep&nbsp;oviAri1</TH>
   <TH>Sheep&nbsp;oviAri1</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>3000</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>2012-03-22</TD><TD ALIGN=RIGHT>15.341%</TD>
   <TD>2012-03-22</TD><TD ALIGN=RIGHT>15.341%</TD>
Line 210: Line 218:
<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>3000</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>2012-03-20</TD><TD ALIGN=RIGHT>27.345%</TD>
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>27.345%</TD>
Line 216: Line 224:
<TR>
<TR>
   <TH>Microbat&nbsp;myoLuc2</TH>
   <TH>Microbat&nbsp;myoLuc2</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>3000</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>2012-03-22</TD><TD ALIGN=RIGHT>24.363%</TD>
   <TD>2012-03-22</TD><TD ALIGN=RIGHT>24.363%</TD>
Line 222: Line 230:
<TR>
<TR>
   <TH>Cat&nbsp;felCat5</TH>
   <TH>Cat&nbsp;felCat5</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>3000</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>2012-04-14</TD><TD ALIGN=RIGHT>29.725%</TD>
   <TD>2012-04-14</TD><TD ALIGN=RIGHT>29.725%</TD>
Line 228: Line 236:
<TR>
<TR>
   <TH>Dog&nbsp;canFam3</TH>
   <TH>Dog&nbsp;canFam3</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>3000</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>2012-03-20</TD><TD ALIGN=RIGHT>29.144%</TD>
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>29.144%</TD>
Line 234: Line 242:
<TR>
<TR>
   <TH>Panda&nbsp;ailMel1</TH>
   <TH>Panda&nbsp;ailMel1</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>3000</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>2012-03-20</TD><TD ALIGN=RIGHT>30.979%</TD>
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>30.979%</TD>
Line 240: Line 248:
<TR>
<TR>
   <TH>Hedgehog&nbsp;eriEur1</TH>
   <TH>Hedgehog&nbsp;eriEur1</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>3000</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>9.856%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>9.856%</TD>
Line 246: Line 254:
<TR>
<TR>
   <TH>Shrew&nbsp;sorAra1</TH>
   <TH>Shrew&nbsp;sorAra1</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>3000</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>9.382%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>9.382%</TD>
Line 252: Line 260:
<TR>
<TR>
   <TH>Sloth&nbsp;choHof1</TH>
   <TH>Sloth&nbsp;choHof1</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>3000</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>2012-03-22</TD><TD ALIGN=RIGHT>18.019%</TD>
   <TD>2012-03-22</TD><TD ALIGN=RIGHT>18.019%</TD>
Line 258: Line 266:
<TR>
<TR>
   <TH>Armadillo&nbsp;dasNov3</TH>
   <TH>Armadillo&nbsp;dasNov3</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>3000</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>2012-04-14</TD><TD ALIGN=RIGHT>25.201%</TD>
   <TD>2012-04-14</TD><TD ALIGN=RIGHT>25.201%</TD>
Line 264: Line 272:
<TR>
<TR>
   <TH>Rock hyrax&nbsp;proCap1</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>3000</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>2012-03-23</TD><TD ALIGN=RIGHT>15.147%</TD>
Line 270: Line 278:
<TR>
<TR>
   <TH>Tenrec&nbsp;echTel1</TH>
   <TH>Tenrec&nbsp;echTel1</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>3000</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>10.947%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>10.947%</TD>
Line 276: Line 284:
<TR>
<TR>
   <TH>Manatee&nbsp;triMan1</TH>
   <TH>Manatee&nbsp;triMan1</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>3000</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>2012-03-30</TD><TD ALIGN=RIGHT>26.546%</TD>
   <TD>2012-03-30</TD><TD ALIGN=RIGHT>26.546%</TD>
Line 282: Line 290:
<TR>
<TR>
   <TH>Elephant&nbsp;loxAfr3</TH>
   <TH>Elephant&nbsp;loxAfr3</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>3000</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>2012-03-20</TD><TD ALIGN=RIGHT>25.823%</TD>
   <TD>2012-03-20</TD><TD ALIGN=RIGHT>25.823%</TD>
Line 288: Line 296:
<TR>
<TR>
   <TH>Wallaby&nbsp;macEug2</TH>
   <TH>Wallaby&nbsp;macEug2</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>3000</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>4.353%</TD>
   <TD>2012-03-24</TD><TD ALIGN=RIGHT>4.353%</TD>

Latest revision as of 21:15, 15 August 2012

See Also


The default
scoring matrix is:
  The HoxD55
scoring matrix is:
 The human-chimp.v2
scoring matrix is:
 The mouse_rat_2.q
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

 
 ACGT
A100-139-54-170
C-13995-83-54
G-54-8395-139
T-170-54-139100

O=600 E=55

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 rn5 yes030003000mouse_rat_2.q 5000lastz-distrib-1.03.02/bin/lastz5520006002 2012-03-2667.353% 70.278%
Squirrel speTri2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1634.217% 39.244%
Kangaroo rat dipOrd1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1619.460% 27.512%
Naked mole rat hetGla2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1432.753% 37.989%
Guinea pig cavPor3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1728.447% 29.115%
Rabbit oryCun2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1725.248% 25.677%
Pika ochPri2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2414.542% 19.908%
Tree shrew tupBel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1719.766% 25.144%
Human hg19 yes030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0838.226% 35.249%
Gorilla gorGor3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0833.987% 34.349%
Chimp panTro4 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1034.674% 31.924%
Gibbon nomLeu2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1434.031% 32.274%
Orangutan ponAbe2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0934.496% 30.610%
Tarsier tarSyr1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1224.560% 24.986%
Chinese rhesus rheMac3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0933.931% 33.464%
Baboon papHam1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1033.577% 32.023%
Bushbaby otoGar3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1329.795% 32.926%
Marmoset calJac3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0932.450% 31.301%
Mouse lemur micMur1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1326.636% 37.574%
Squirrel monkey saiBol1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-0932.339% 33.848%
Horse equCab2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1634.415% 37.138%
Alpaca vicPac1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-1722.636% 31.769%
Dolphin turTru2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1430.267% 33.492%
Pig susScr3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1425.685% 29.445%
Cow bosTau7 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2226.255% 25.383%
Sheep oviAri1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2215.341% 31.925%
Megabat pteVam1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2027.345% 38.627%
Microbat myoLuc2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2224.363% 33.650%
Cat felCat5 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1429.725% 32.244%
Dog canFam3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2029.144% 31.624%
Panda ailMel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2030.979% 35.562%
Hedgehog eriEur1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-249.856% 12.264%
Shrew sorAra1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-249.382% 13.569%
Sloth choHof1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2218.019% 23.687%
Armadillo dasNov3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-1425.201% 21.066%
Rock hyrax proCap1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2315.147% 16.214%
Tenrec echTel1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2410.947% 14.117%
Manatee triMan1 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-3026.546% 24.649%
Elephant loxAfr3 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-2025.823% 21.616%
Wallaby macEug2 no030003000default 9400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-244.353% 4.448%
Tasmanian devil sarHar1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-308.479% 7.888%
Opossum monDom5 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-309.584% 7.205%
Platypus ornAna1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-305.348% 7.334%
Chicken galGal4 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.676% 8.100%
Zebra finch taeGut1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.599% 7.304%
Turkey melGal1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.511% 8.211%
Budgerigar melUnd1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-303.589% 7.350%
Lizard anoCar2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.331% 4.988%
Painted turtle chrPic1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-03-304.731% 5.488%
X. tropicalis xenTro3 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-033.125% 6.651%
Coelacanth latCha1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-032.715% 3.380%
Atlantic cod gadMor1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-031.726% 6.810%
Stickleback gasAcu1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-032.016% 10.927%
Fugu fr3 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-031.789% 12.134%
Nile tilapia oreNil2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-111.957% 6.091%
Tetraodon tetNig2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-021.735% 13.642%
Zebrafish danRer7 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-032.602% 5.107%
Medaka oryLat2 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-031.936% 6.561%
Lamprey petMar1 no022006000HoxD55.q 3400lastz-distrib-1.03.02/bin/lastz3020004001 2012-04-041.101% 3.159%