Index: src/hg/makeDb/trackDb/trackDb.chainNet.ra
===================================================================
RCS file: /projects/compbio/cvsroot/kent/src/hg/makeDb/trackDb/trackDb.chainNet.ra,v
retrieving revision 1.8
retrieving revision 1.9
diff -b -B -U 1000000 -r1.8 -r1.9
--- src/hg/makeDb/trackDb/trackDb.chainNet.ra	18 Dec 2009 20:19:46 -0000	1.8
+++ src/hg/makeDb/trackDb/trackDb.chainNet.ra	18 Dec 2009 23:41:19 -0000	1.9
@@ -1,1011 +1,1053 @@
 #	"$Id$";
 
 # release alpha until individual fr2 tracks are obsolete
 track chainNetFr2
 release alpha
 compositeTrack on
 shortLabel Fugu Chain/Net
 longLabel Fugu (Oct. 2004/fr2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 159
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb fr2
 chainMinScore 5000
 chainLinearGap loose
 spectrum on
 html chainNet
 
     track chainFr2
     release alpha
     subTrack chainNetFr2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain fr2
 
     track netFr2
     release alpha
     subTrack chainNetFr2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign fr2 chainFr2
 
 track chainNetTetNig2
 compositeTrack on
 shortLabel Tetraodon Chain/Net
 longLabel Tetraodon (Mar. 2007/tetNig2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 159
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb tetNig2
 chainMinScore 5000
 chainLinearGap loose
 spectrum on
 html chainNet
 
     track chainTetNig2
     subTrack chainNetTetNig2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain tetNig2
 
     track netTetNig2
     subTrack chainNetTetNig2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign tetNig2 chainTetNig2
 
 track chainNetDanRer6
 compositeTrack on
 shortLabel Zebrafish Chain/Net
 longLabel Zebrafish (Dec. 2008/danRer6), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 159
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb danRer6
 chainMinScore 5000
 chainLinearGap loose
 spectrum on
 html chainNet
 
     track chainDanRer6
     subTrack chainNetDanRer6
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain danRer6
 
     track netDanRer6
     subTrack chainNetDanRer6
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign danRer6 chainDanRer6
 
 # release alpha until individual oryLat2 tracks are obsolete
 track chainNetOryLat2
 release alpha
 compositeTrack on
 shortLabel Medaka Chain/Net
 longLabel Medaka (Oct. 2005/oryLat2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 165.5
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb oryLat2
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
     track chainOryLat2
     release alpha
     subTrack chainNetOryLat2
     subGroups view=chain
     shortLabel $o_Organism Chain 
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain oryLat2
     otherDb oryLat2
 
     track netOryLat2
     release alpha
     subTrack chainNetOryLat2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign oryLat2 chainOryLat2
     otherDb oryLat2
 
 # release alpha until individual gasAcu1 tracks are obsolete
 track chainNetGasAcu1
 release alpha
 compositeTrack on
 shortLabel Stickleback Chain/Net
 longLabel Stickleback (Feb 2006/gasAcu1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 181
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb gasAcu1
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainGasAcu1
     release alpha
     subTrack chainNetGasAcu1
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain gasAcu1
 
     track netGasAcu1
     release alpha
     subTrack chainNetGasAcu1
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign gasAcu1 chainGasAcu1
 
+# release alpha until individual galGal2 tracks are obsolete
+track chainNetGalGal2
+release alpha
+compositeTrack on
+shortLabel Chicken Chain/Net
+longLabel Chicken (Feb 2004/galGal2), Chain and Net Alignments
+subGroup1 view Views chain=Chain net=Net
+dragAndDrop subTracks
+visibility hide
+visibilityViewDefaults chain=pack net=dense
+group compGeno
+noInherit on
+priority 181
+color 0,0,0
+altColor 255,255,0
+type bed 3
+settingsByView chain:spectrum=on
+sortOrder view=+
+matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
+matrixHeader A, C, G, T
+otherDb galGal2
+chainMinScore 5000
+chainLinearGap loose
+spectrum on
+html chainNet
+
+    track chainGalGal2
+    release alpha
+    subTrack chainNetGalGal2
+    subGroups view=chain
+    shortLabel $o_Organism Chain
+    longLabel $o_Organism ($o_date/$o_db) Chained Alignments
+    type chain galGal2
+
+    track netGalGal2
+    release alpha
+    subTrack chainNetGalGal2
+    subGroups view=net
+    shortLabel $o_Organism Net
+    longLabel $o_Organism ($o_date/$o_db) Alignment Net
+    type netAlign galGal2 chainGalGal2
+
 # release alpha until individual galGal3 tracks are obsolete
 track chainNetGalGal3
 release alpha
 compositeTrack on
 shortLabel Chicken Chain/Net
 longLabel Chicken (May 2006/galGal3), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 181
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb galGal3
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainGalGal3
     release alpha
     subTrack chainNetGalGal3
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain galGal3
 
     track netGalGal3
     release alpha
     subTrack chainNetGalGal3
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign galGal3 chainGalGal3
 
 # release alpha until ornAna1 individual chain/net tracks phased out
 track chainNetOrnAna1
 release alpha
 compositeTrack on
 shortLabel Platypus Chain/Net
 longLabel Platypus (Mar. 2007/ornAna1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 191
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb ornAna1
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainOrnAna1
     release alpha
     subTrack chainNetOrnAna1
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain ornAna1
 
     track netOrnAna1
     release alpha
     subTrack chainNetOrnAna1
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign ornAna1 chainOrnAna1
 
 track chainNetMonDom1
 release alpha
 compositeTrack on
 shortLabel Opossum Chain/Net
 longLabel Opossum (Oct. 2004/monDom1), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 191
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb monDom1
 chainMinScore 5000
 chainLinearGap loose
 spectrum on
 html chainNet
 
     track chainMonDom1
     release alpha
     subTrack chainNetMonDom1
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain monDom1
 
     track netMonDom1
     release alpha
     subTrack chainNetMonDom1
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign monDom1 chainMonDom1
 
 track chainNetMonDom4
 release alpha
 compositeTrack on
 shortLabel Opossum Chain/Net
 longLabel Opossum (Jan. 2006/monDom4), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 191
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
 matrixHeader A, C, G, T
 otherDb monDom4
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainMonDom4
     release alpha
     subTrack chainNetMonDom4
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain monDom4
 
     track netMonDom4
     release alpha
     subTrack chainNetMonDom4
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign monDom4 chainMonDom4
 
 track chainNetMonDom5
 compositeTrack on
 shortLabel Opossum Chain/Net
 longLabel Opossum (Oct. 2006/monDom5), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 191
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb monDom5
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainMonDom5
     subTrack chainNetMonDom5
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain monDom5
 
     track netMonDom5
     subTrack chainNetMonDom5
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign monDom5 chainMonDom5
 
 # release alpha until mm9 individual chain/net tracks phased out
 track chainNetMm9
 release alpha
 compositeTrack on
 shortLabel Mouse Chain/Net
 longLabel Mouse (Jul. 2007/mm9), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 209
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb mm9
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainMm9
     release alpha
     subTrack chainNetMm9
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain mm9
 
     track netMm9
     release alpha
     subTrack chainNetMm9
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign mm9 chainMm9
 
 # release alpha until rn4 individual chain/net tracks phased out
 track chainNetRn4
 release alpha
 compositeTrack on
 shortLabel Rat Chain/Net
 longLabel Rat (Nov. 2004/rn4), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 209
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb rn4
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainRn4
     release alpha
     subTrack chainNetRn4
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain rn4
 
     track netRn4
     release alpha
     subTrack chainNetRn4
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign rn4 chainRn4
 
 track chainNetEquCab2
 compositeTrack on
 shortLabel Horse Chain/Net
 longLabel Horse (Sep. 2007/equCab2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 240
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb equCab2
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainEquCab2
     subTrack chainNetEquCab2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain equCab2
 
     track netEquCab2
     subTrack chainNetEquCab2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign equCab2 chainEquCab2
 
 # release alpha until bosTau4 individual tracks phased out
 track chainNetBosTau4
 release alpha
 compositeTrack on
 shortLabel Cow Chain/Net
 longLabel Cow (Oct. 2007/bosTau4), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 240
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb bosTau4
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainBosTau4
     release alpha
     subTrack chainNetBosTau4
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain bosTau4
 
     track netBosTau4
     release alpha
     subTrack chainNetBosTau4
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign bosTau4 chainBosTau4
 
 # release alpha until bosTau3 individual tracks phased out
 track chainNetBosTau3
 release alpha
 compositeTrack on
 shortLabel Cow Chain/Net
 longLabel Cow (Aug. 2006/bosTau3), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 240
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb bosTau3
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainBosTau3
     release alpha
     subTrack chainNetBosTau3
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain bosTau3
 
     track netBosTau3
     release alpha
     subTrack chainNetBosTau3
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign bosTau3 chainBosTau3
 
 # release alpha until bosTau2 individual tracks phased out
 track chainNetBosTau2
 release alpha
 compositeTrack on
 shortLabel Cow Chain/Net
 longLabel Cow (Mar. 2005/bosTau2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 240
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb bosTau2
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainBosTau2
     release alpha
     subTrack chainNetBosTau2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain bosTau2
 
     track netBosTau2
     release alpha
     subTrack chainNetBosTau2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign bosTau2 chainBosTau2
 
 # release alpha until canFam2 individual tracks phased out
 track chainNetCanFam2
 release alpha
 compositeTrack on
 shortLabel Dog Chain/Net
 longLabel Dog (May 2005/canFam2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 240
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb canFam2
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainCanFam2
     release alpha
     subTrack chainNetCanFam2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain canFam2
 
     track netCanFam2
     release alpha
     subTrack chainNetCanFam2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign canFam2 chainCanFam2
 
 # release alpha until felCat3 individual tracks phased out
 track chainNetFelCat3
 release alpha
 compositeTrack on
 shortLabel Cat Chain/Net
 longLabel Cat (Mar. 2006/felCat3), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 240
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb felCat3
 chainMinScore 3000
 chainLinearGap medium
 spectrum on
 html chainNet
 
     track chainFelCat3
     release alpha
     subTrack chainNetFelCat3
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain felCat3
 
     track netFelCat3
     release alpha
     subTrack chainNetFelCat3
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign felCat3 chainFelCat3
 
 track chainNetVenter
 compositeTrack on
 shortLabel Venter Chain/Net
 longLabel J. Craig Venter Chain and Net Alignments
 subGroup1 view Views chain=Chains net=Nets
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 500
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 
     track chainVenter1
     subTrack chainNetVenter off
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     color 100,50,0
     altColor 255,240,200
     matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
     matrixHeader A, C, G, T
     type chain venter1
     otherDb venter1
 
     track netVenter1
     subTrack chainNetVenter off
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign venter1 chainVenter1
     otherDb venter1
 
 track chainNetHg18
 release alpha
 compositeTrack on
 shortLabel Human Chain/Net
 longLabel Human (Mar. 2006/hg18), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 498
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
 matrixHeader A, C, G, T
 otherDb hg18
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
     track chainHg18
     release alpha
     subTrack chainNetHg18
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain hg18
 
     track netHg18
     release alpha
     subTrack chainNetHg18
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment net
     type netAlign hg18 chainHg18
 
 track chainNetHg19
 compositeTrack on
 shortLabel Human Chain/Net
 longLabel Human (Feb. 2009/hg19), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 498
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
 matrixHeader A, C, G, T
 otherDb hg19
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
     track chainHg19
     subTrack chainNetHg19
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain hg19
 
     track netHg19
     subTrack chainNetHg19
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment net
     type netAlign hg19 chainHg19
 
 track chainNetPanTro2
 release alpha
 compositeTrack on
 shortLabel Chimp Chain/Net
 longLabel Chimp (Mar. 2006/panTro2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 498
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
 matrixHeader A, C, G, T
 otherDb panTro2
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
     track chainPanTro2
     release alpha
     subTrack chainNetPanTro2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain panTro2
 
     track netPanTro2
     release alpha
     subTrack chainNetPanTro2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment net
     type netAlign panTro2 chainPanTro2
 
 track chainNetPonAbe2
 release alpha
 compositeTrack on
 shortLabel Orangutan Chain/Net
 longLabel Orangutan (Jul. 2007/ponAbe2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 498
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 90,-330,-236,-356,-330,100,-318,-236,-236,-318,100,-330,-356,-236,-330,90
 matrixHeader A, C, G, T
 otherDb ponAbe2
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
     track chainPonAbe2
     release alpha
     subTrack chainNetPonAbe2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain ponAbe2
 
     track netPonAbe2
     release alpha
     subTrack chainNetPonAbe2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment net
     type netAlign ponAbe2 chainPonAbe2
 
 track chainNetRheMac2
 release alpha
 compositeTrack on
 shortLabel Rhesus Chain/Net
 longLabel Rhesus (Jan. 2006/rheMac2), Chain and Net Alignments
 subGroup1 view Views chain=Chain net=Net
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 498
 color 100,50,0
 altColor 255,240,200
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 matrix 16 91,-114,-31,-123,-114,100,-125,-31,-31,-125,100,-114,-123,-31,-114,91
 matrixHeader A, C, G, T
 otherDb rheMac2
 chainMinScore 3000
 chainLinearGap medium
 html chainNet
 
     track chainRheMac2
     release alpha
     subTrack chainNetRheMac2
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     type chain rheMac2
 
     track netRheMac2
     release alpha
     subTrack chainNetRheMac2
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment net
     type netAlign rheMac2 chainRheMac2
 
 track chainNetPoodle
 compositeTrack on
 shortLabel Poodle Chain/Net
 longLabel Poodle Chain and Net Alignments
 subGroup1 view Views chain=Chains net=Nets
 dragAndDrop subTracks
 visibility hide
 visibilityViewDefaults chain=pack net=dense
 group compGeno
 noInherit on
 priority 500
 color 0,0,0
 altColor 255,255,0
 type bed 3
 settingsByView chain:spectrum=on
 sortOrder view=+
 
     track chainCanFamPoodle1
     subTrack chainNetPoodle off
     subGroups view=chain
     shortLabel $o_Organism Chain
     longLabel $o_Organism ($o_date/$o_db) Chained Alignments
     color 100,50,0
     altColor 255,240,200
     matrix 16 91,-90,-25,-100,-90,100,-100,-25,-25,-100,100,-90,-100,-25,-90,91
     matrixHeader A, C, G, T
     type chain canFamPoodle1
     otherDb canFamPoodle1
 
     track netCanFamPoodle1
     subTrack chainNetPoodle off
     subGroups view=net
     shortLabel $o_Organism Net
     longLabel $o_Organism ($o_date/$o_db) Alignment Net
     type netAlign canFamPoodle1 chainCanFamPoodle1
     otherDb canFamPoodle1

