Java version: 1.5.0_18
sparc SunOS 5.10
Error reading properties file: java.io.FileNotFoundException: /home/psgendb/.jalview_properties (No such file or directory)
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
(C) 2003-2007 Jmol Development
Jmol Version 11.0.2  2007-04-24 19:38
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_18
os.name:SunOS


FileManager.openFile(/var/tmp/jalview_pdb4232821374157862840.txt,0,0,0,0)
FileManager opening /var/tmp/jalview_pdb4232821374157862840.txt
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:het: FES
SmarterJmolAdapter:hetero: FES FE2/S2 (INORGANIC) CLUSTER
SmarterJmolAdapter:setunitcellitem 6 0.032257996
SmarterJmolAdapter:setunitcellitem 7 0.0
SmarterJmolAdapter:setunitcellitem 8 0.0
SmarterJmolAdapter:setunitcellitem 9 0.0
SmarterJmolAdapter:setunitcellitem 10 0.0
SmarterJmolAdapter:setunitcellitem 11 0.025523
SmarterJmolAdapter:setunitcellitem 12 0.0
SmarterJmolAdapter:setunitcellitem 13 0.0
SmarterJmolAdapter:setunitcellitem 14 0.0
SmarterJmolAdapter:setunitcellitem 15 0.0
SmarterJmolAdapter:setunitcellitem 16 0.011973
SmarterJmolAdapter:setunitcellitem 17 0.0
openFile(/var/tmp/jalview_pdb4232821374157862840.txt,0,0,0,0)130 ms
frame: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
measurement[0] = [2, 734, 664, 1.328 nm]
INFO - Not enabling Google Tracking.
INFO - http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred Job Id '/jobs/www-jpred/jp_C63fBED'
Verifying against UNIPROT
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
INFO - Loading mapping descriptors from jar:file:/home/psgendb/java/Jalview2.4/jalview.jar!/uniprot_mapping.xml
Error getUniprotEntries() Premature end of file.
Verifying against PDB
Ignoring invalid pdb query: 'AF11'
Ignoring invalid pdb query: 'AF12'
Ignoring invalid pdb query: 'GMU1'
Ignoring invalid pdb query: 'BOAJ'
Ignoring invalid pdb query: 'BOAJ'
Ignoring invalid pdb query: 'ZMA1'
Verifying against UniProtKB/TrEMBL
No proxy for UniProtKB/TrEMBL
INFO - http://www.compbio.dundee.ac.uk/JalviewWS/services/jpred Job Id '/jobs/www-jpred/jp_vzxFzSs'
Java version: 1.5.0_18
sparc SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/GDE/multalign/bio2913166016992685367.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_18
sparc SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/GDE/multalign/bio4432435374727566541.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio8223387435939781574.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio8223387435939781574.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio8223387435939781574.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio7679800766673663058.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio7679800766673663058.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio7679800766673663058.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio2323496225087752551.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio2323496225087752551.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio2323496225087752551.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio3388800925813481725.tmp.fsa
INFO - Not enabling Google Tracking.
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio3388800925813481725.tmp.fsa
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio3388800925813481725.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
INFO - Not enabling Google Tracking.
(C) 2003-2007 Jmol Development
Jmol Version 11.0.2  2007-04-24 19:38
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_22
os.name:SunOS


FileManager.openFile(/var/tmp/jalview_pdb6651689386596226.txt,0,0,0,0)
FileManager opening /var/tmp/jalview_pdb6651689386596226.txt
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:het: FES
SmarterJmolAdapter:hetero: FES FE2/S2 (INORGANIC) CLUSTER
SmarterJmolAdapter:setunitcellitem 6 0.032257996
SmarterJmolAdapter:setunitcellitem 7 0.0
SmarterJmolAdapter:setunitcellitem 8 0.0
SmarterJmolAdapter:setunitcellitem 9 0.0
SmarterJmolAdapter:setunitcellitem 10 0.0
SmarterJmolAdapter:setunitcellitem 11 0.025523
SmarterJmolAdapter:setunitcellitem 12 0.0
SmarterJmolAdapter:setunitcellitem 13 0.0
SmarterJmolAdapter:setunitcellitem 14 0.0
SmarterJmolAdapter:setunitcellitem 15 0.0
SmarterJmolAdapter:setunitcellitem 16 0.011973
SmarterJmolAdapter:setunitcellitem 17 0.0
openFile(/var/tmp/jalview_pdb6651689386596226.txt,0,0,0,0)46 ms
frame: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
measurement[0] = [2, 734, 664, 1.328 nm]
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
INFO - Not enabling Google Tracking.
(C) 2003-2007 Jmol Development
Jmol Version 11.0.2  2007-04-24 19:38
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_22
os.name:SunOS


FileManager.openFile(/var/tmp/jalview_pdb3910646236837160290.txt,0,0,0,0)
FileManager opening /var/tmp/jalview_pdb3910646236837160290.txt
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:het: FES
SmarterJmolAdapter:hetero: FES FE2/S2 (INORGANIC) CLUSTER
SmarterJmolAdapter:setunitcellitem 6 0.032257996
SmarterJmolAdapter:setunitcellitem 7 0.0
SmarterJmolAdapter:setunitcellitem 8 0.0
SmarterJmolAdapter:setunitcellitem 9 0.0
SmarterJmolAdapter:setunitcellitem 10 0.0
SmarterJmolAdapter:setunitcellitem 11 0.025523
SmarterJmolAdapter:setunitcellitem 12 0.0
SmarterJmolAdapter:setunitcellitem 13 0.0
SmarterJmolAdapter:setunitcellitem 14 0.0
SmarterJmolAdapter:setunitcellitem 15 0.0
SmarterJmolAdapter:setunitcellitem 16 0.011973
SmarterJmolAdapter:setunitcellitem 17 0.0
openFile(/var/tmp/jalview_pdb3910646236837160290.txt,0,0,0,0)55 ms
frame: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
measurement[0] = [2, 734, 664, 1.328 nm]
Exception in thread "AWT-EventQueue-0" java.lang.ArrayIndexOutOfBoundsException: No such child: 4
	at java.awt.Container.getComponent(Container.java:280)
	at javax.swing.JComponent.rectangleIsObscured(JComponent.java:4126)
	at javax.swing.JComponent.paint(JComponent.java:998)
	at javax.swing.JLayeredPane.paint(JLayeredPane.java:559)
	at javax.swing.JComponent.paintWithOffscreenBuffer(JComponent.java:4966)
	at javax.swing.JComponent.paintDoubleBuffered(JComponent.java:4919)
	at javax.swing.JComponent._paintImmediately(JComponent.java:4862)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4669)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:451)
	at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:110)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
	at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign/defensin.tcoffee.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio1038959599691723668.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio1038959599691723668.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio1038959599691723668.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio1469144025345414384.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio1469144025345414384.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio1469144025345414384.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio1667562006705121070.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio1667562006705121070.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio1667562006705121070.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio6961423279615066383.tmp.fsa
Can't find /home/psgendb/tutorials/bioLegato/multalign//home/psgendb/public_html/tutorials/bioLegato/multalign/bio6961423279615066383.tmp.fsa
INFO - Not enabling Google Tracking.
Error whilst identifying
java.io.IOException: Problem opening /home/psgendb/tutorials/bioLegato/multalign/home/psgendb/public_html/tutorials/bioLegato/multalign/bio6961423279615066383.tmp.fsa : FILE CANNOT BE OPENED FOR READING
	at jalview.io.FileParse.<init>(FileParse.java:189)
	at jalview.io.IdentifyFile.Identify(IdentifyFile.java:50)
	at jalview.bin.Jalview.main(Jalview.java:206)
	at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
	at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39)
	at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)
	at java.lang.reflect.Method.invoke(Method.java:592)
	at com.zerog.lax.LAX.launch(DashoA10*..)
	at com.zerog.lax.LAX.main(DashoA10*..)
error
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
INFO - Not enabling Google Tracking.
(C) 2003-2007 Jmol Development
Jmol Version 11.0.2  2007-04-24 19:38
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_22
os.name:SunOS


FileManager.openFile(/var/tmp/jalview_pdb3905690986033794191.txt,0,0,0,0)
FileManager opening /var/tmp/jalview_pdb3905690986033794191.txt
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:het: FES
SmarterJmolAdapter:hetero: FES FE2/S2 (INORGANIC) CLUSTER
SmarterJmolAdapter:setunitcellitem 6 0.032257996
SmarterJmolAdapter:setunitcellitem 7 0.0
SmarterJmolAdapter:setunitcellitem 8 0.0
SmarterJmolAdapter:setunitcellitem 9 0.0
SmarterJmolAdapter:setunitcellitem 10 0.0
SmarterJmolAdapter:setunitcellitem 11 0.025523
SmarterJmolAdapter:setunitcellitem 12 0.0
SmarterJmolAdapter:setunitcellitem 13 0.0
SmarterJmolAdapter:setunitcellitem 14 0.0
SmarterJmolAdapter:setunitcellitem 15 0.0
SmarterJmolAdapter:setunitcellitem 16 0.011973
SmarterJmolAdapter:setunitcellitem 17 0.0
openFile(/var/tmp/jalview_pdb3905690986033794191.txt,0,0,0,0)47 ms
frame: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
measurement[0] = [2, 734, 664, 1.328 nm]
Exception in thread "Thread-14" java.lang.NullPointerException
	at jalview.gui.AlignViewport$ConsensusThread.run(AlignViewport.java:577)
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/public_html/tutorials/bioLegato/multalign/bio3462449024405879267.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/public_html/tutorials/bioLegato/multalign/bio2698269472231839984.tmp.fsa
INFO - Not enabling Google Tracking.
Score = 2260
Length of alignment = 86
Sequence AF128239_CDS1 :  1 - 107 (Sequence length = 107)
Sequence AF112443_CDS1 :  1 - 84 (Sequence length = 84)

AF128239_CDS1 MARSIYFMAFLVLAVTLFVANGVQGQNNICKTTSKHFKGLCFADSKCRKVCIQEDKFE
              ||||||||||||||.||||| ||||..  ||  .|  |  | .|. |.|.|.. .|.|
AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKELTKPVK--CSSDPLCQKLCMEKEKYE

AF128239_CDS1 DGHCSKLQRKCLCTKNCVFDNIPNDVGT
              ||||  .  |||| | |    .. .. .
AF112443_CDS1 DGHCFTILSKCLCMKRCNAKTLATELLA

Percentage ID = 51.16

Score = 100
Length of alignment = 80
Sequence BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)
Sequence AF112443_CDS1 :  1 - 84 (Sequence length = 84)

BOAJ5280_CDS1 NTVKLSLIGFVMLTVLLLGETVIAQKRKPCYS-QEPDKTCEVNRCKANCVKKHKKILA
               .  . ...|..|.. |.    .  |   |     | |      |.  |. |  |   
AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKELTKPVKCSSDPLCQKLCMEK-EK-YE

BOAJ5280_CDS1 FTSCIKENNGNMYCRCQYPCPP
                 |.   .    | |   | .
AF112443_CDS1 DGHCFTILSK---CLCMKRCNA

Percentage ID = 18.75

Score = 70
Length of alignment = 28
Sequence BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)
Sequence AF128239_CDS1 :  1 - 107 (Sequence length = 107)

BOAJ5280_CDS1 MKNTVKLSLIGFVM-LTVLLLGETVIAQ
              . | |   |.     |   || | ... 
AF128239_CDS1 IPNDVGTILVQDAKTLEAQLLEEEILGL

Percentage ID = 25.00

Score = 100
Length of alignment = 80
Sequence BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)
Sequence AF112443_CDS1 :  1 - 84 (Sequence length = 84)

BOAJ5281_CDS1 NTVKLSLIGFVMLTVLLLGETVIAQKRKPCYS-QEPDKTCEVNRCKANCVKKHKKILA
               .  . ...|..|.. |.    .  |   |     | |      |.  |. |  |   
AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKELTKPVKCSSDPLCQKLCMEK-EK-YE

BOAJ5281_CDS1 FTSCIKENNGNMYCRCQYPCPP
                 |.   .    | |   | .
AF112443_CDS1 DGHCFTILSK---CLCMKRCNA

Percentage ID = 18.75

Score = 70
Length of alignment = 28
Sequence BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)
Sequence AF128239_CDS1 :  1 - 107 (Sequence length = 107)

BOAJ5281_CDS1 MKNTVKLSLIGFVM-LTVLLLGETVIAQ
              . | |   |.     |   || | ... 
AF128239_CDS1 IPNDVGTILVQDAKTLEAQLLEEEILGL

Percentage ID = 25.00

Score = 4450
Length of alignment = 81
Sequence BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)
Sequence BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)

BOAJ5281_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHKKIL
              ||||||||||||||||||||||||||||||||||||||||||||||||||||||||||
BOAJ5280_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHKKIL

BOAJ5281_CDS1 AFTSCIKENNGNMYCRCQYPCPP
              |||||||||||||||||||||||
BOAJ5280_CDS1 AFTSCIKENNGNMYCRCQYPCPP

Percentage ID = 100.00

Score = 720
Length of alignment = 75
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)
Sequence  AF112443_CDS1 :  1 - 84 (Sequence length = 84)

CAGTHIOGN_CDS1 MAGFSKVIATIFLMMMLVFATGMVAEARTCESQSHRFKGLCFSKSNCGSVC-HTEGF
               ||     .| . | | |  | |. .    |   .   |  | | . |  .| . | .
 AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKELTKPVK--CSSDPLCQKLCMEKEKY

CAGTHIOGN_CDS1 NGGHCRGFRRRCFCTRHC
               ..|||  .  .|.| ..|
 AF112443_CDS1 EDGHCFTILSKCLCMKRC

Percentage ID = 28.00

Score = 1460
Length of alignment = 75
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)
Sequence  AF128239_CDS1 :  1 - 107 (Sequence length = 107)

CAGTHIOGN_CDS1 MAGFSKVIATIFLMMMLVFATGMVAEARTCESQSHRFKGLCFSKSNCGSVCHTEG-F
               ||     .| . | . |  | |. ..   | . | .||||||. |.|  ||  |. |
 AF128239_CDS1 MARSIYFMAFLVLAVTLFVANGVQGQNNICKTTSKHFKGLCFADSKCRKVCIQEDKF

CAGTHIOGN_CDS1 NGGHCRGFRRRCFCTRHC
               ..|||  ..|.|.||..|
 AF128239_CDS1 EDGHCSKLQRKCLCTKNC

Percentage ID = 38.67

Score = 60
Length of alignment = 83
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)
Sequence  BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)

CAGTHIOGN_CDS1 MAGFSKV--IATIFLMMMLVFATGMVAEARTCESQ----S---HRFKGLCFSKSNCG
               |    |.  |. . | ..|.  | .    . | ||    .   .| |. |  | .  
 BOAJ5280_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHK-K

CAGTHIOGN_CDS1 SVCHTEGFNGGHCRGFRRRCFCTRHC
                .  |  ..  .   . |   |   |
 BOAJ5280_CDS1 ILAFTSCIKENNGNMYCR---CQYPC

Percentage ID = 20.48

Score = 60
Length of alignment = 83
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)
Sequence  BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)

CAGTHIOGN_CDS1 MAGFSKV--IATIFLMMMLVFATGMVAEARTCESQ----S---HRFKGLCFSKSNCG
               |    |.  |. . | ..|.  | .    . | ||    .   .| |. |  | .  
 BOAJ5281_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHK-K

CAGTHIOGN_CDS1 SVCHTEGFNGGHCRGFRRRCFCTRHC
                .  |  ..  .   . |   |   |
 BOAJ5281_CDS1 ILAFTSCIKENNGNMYCR---CQYPC

Percentage ID = 20.48

Score = 500
Length of alignment = 76
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)
Sequence  AF112443_CDS1 :  1 - 84 (Sequence length = 84)

CAGTHIOGN_CDS2 MAGFSKVIATIFLMMMLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVC-RREGF
               ||     .| . | | |  | .. .    |  |.   |  | |   | ..|  .| .
 AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKELTKPVK--CSSDPLCQKLCMEKEKY

CAGTHIOGN_CDS2 TSGVCRGFPLKCFCRKPGA
                 | |  .  ||.| |   
 AF112443_CDS1 EDGHCFTILSKCLCMKRCN

Percentage ID = 27.63

Score = 1010
Length of alignment = 76
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)
Sequence  AF128239_CDS1 :  1 - 107 (Sequence length = 107)

CAGTHIOGN_CDS2 MAGFSKVIATIFLMMMLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVCRREG-F
               ||     .| . | . |  | .. .. .|| . | .|||||..   | .|| .|. |
 AF128239_CDS1 MARSIYFMAFLVLAVTLFVANGVQGQNNICKTTSKHFKGLCFADSKCRKVCIQEDKF

CAGTHIOGN_CDS2 TSGVCRGFPLKCFCRKPGA
                 | |  .  ||.| |   
 AF128239_CDS1 EDGHCSKLQRKCLCTKNCV

Percentage ID = 32.89

Score = 60
Length of alignment = 80
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)
Sequence  BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)

CAGTHIOGN_CDS2 MAGFSKV--IATIFLMMMLVFATDMMAEAKICEALSGNFKGLCLSSR-DCGNVCRRE
               |    |.  |. . | ..|.  | .    | | .   .        . .| .  .. 
 BOAJ5280_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHKKI

CAGTHIOGN_CDS2 -GFTSGVCRGFP-LKCFCRKPGA
                .||| .      . | |. | .
 BOAJ5280_CDS1 LAFTSCIKENNGNMYCRCQYPCP

Percentage ID = 18.75

Score = 60
Length of alignment = 80
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)
Sequence  BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)

CAGTHIOGN_CDS2 MAGFSKV--IATIFLMMMLVFATDMMAEAKICEALSGNFKGLCLSSR-DCGNVCRRE
               |    |.  |. . | ..|.  | .    | | .   .        . .| .  .. 
 BOAJ5281_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHKKI

CAGTHIOGN_CDS2 -GFTSGVCRGFP-LKCFCRKPGA
                .||| .      . | |. | .
 BOAJ5281_CDS1 LAFTSCIKENNGNMYCRCQYPCP

Percentage ID = 18.75

Score = 2590
Length of alignment = 74
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)

CAGTHIOGN_CDS2 MAGFSKVIATIFLMMMLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVCRREGFT
               |||||||||||||||||||||.|.|||. ||. |  |||||.|  .||.||. ||| 
CAGTHIOGN_CDS1 MAGFSKVIATIFLMMMLVFATGMVAEARTCESQSHRFKGLCFSKSNCGSVCHTEGFN

CAGTHIOGN_CDS2 SGVCRGFPLKCFCRKPG
               .| ||||  .||| .  
CAGTHIOGN_CDS1 GGHCRGFRRRCFCTRHC

Percentage ID = 66.22

Score = 700
Length of alignment = 76
Sequence     CAGT_CDS1 :  1 - 75 (Sequence length = 75)
Sequence AF112443_CDS1 :  1 - 84 (Sequence length = 84)

    CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVC-RREGFT
              ||     .| . | | |  | .. .    |  |.   |  | |   | ..|  .| . 
AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKELTKPVK--CSSDPLCQKLCMEKEKYE

    CAGT_CDS1 DGSCIGFRLQCFCTKPCA
              || |. .  .|.| | | 
AF112443_CDS1 DGHCFTILSKCLCMKRCN

Percentage ID = 28.95

Score = 1240
Length of alignment = 76
Sequence     CAGT_CDS1 :  1 - 75 (Sequence length = 75)
Sequence AF128239_CDS1 :  1 - 107 (Sequence length = 107)

    CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVCRREG-FT
              ||     .| . | . |  | .. .. .|| . | .|||||..   | .|| .|. | 
AF128239_CDS1 MARSIYFMAFLVLAVTLFVANGVQGQNNICKTTSKHFKGLCFADSKCRKVCIQEDKFE

    CAGT_CDS1 DGSCIGFRLQCFCTKPCA
              || |  .. .|.||| | 
AF128239_CDS1 DGHCSKLQRKCLCTKNCV

Percentage ID = 35.53

Score = 170
Length of alignment = 80
Sequence     CAGT_CDS1 :  1 - 75 (Sequence length = 75)
Sequence BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)

    CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMMAEAKICEALSGNFKGLCLSSRDCGN-VCRREG-F
              |    |.    |.|. ...  . .   |     | .    |  .|  .| | ..   .
BOAJ5280_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHKKIL

    CAGT_CDS1 TDGSCI---GFRLQCFCTKPCA
              .  |||      . | |  ||.
BOAJ5280_CDS1 AFTSCIKENNGNMYCRCQYPCP

Percentage ID = 21.25

Score = 170
Length of alignment = 80
Sequence     CAGT_CDS1 :  1 - 75 (Sequence length = 75)
Sequence BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)

    CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMMAEAKICEALSGNFKGLCLSSRDCGN-VCRREG-F
              |    |.    |.|. ...  . .   |     | .    |  .|  .| | ..   .
BOAJ5281_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQEPDKTCEVNRCKANCVKKHKKIL

    CAGT_CDS1 TDGSCI---GFRLQCFCTKPCA
              .  |||      . | |  ||.
BOAJ5281_CDS1 AFTSCIKENNGNMYCRCQYPCP

Percentage ID = 21.25

Score = 2720
Length of alignment = 74
Sequence      CAGT_CDS1 :  1 - 75 (Sequence length = 75)
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)

     CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVCRREGFT
               |||||||.|||||||.|||||.|.|||. ||. |  |||||.|  .||.||. ||| 
CAGTHIOGN_CDS1 MAGFSKVIATIFLMMMLVFATGMVAEARTCESQSHRFKGLCFSKSNCGSVCHTEGFN

     CAGT_CDS1 DGSCIGFRLQCFCTKPC
               .| | ||| .||||. |
CAGTHIOGN_CDS1 GGHCRGFRRRCFCTRHC

Percentage ID = 66.22

Score = 3510
Length of alignment = 75
Sequence      CAGT_CDS1 :  1 - 75 (Sequence length = 75)
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)

     CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVCRREGFT
               |||||||.|||||||.|||||||||||||||||||||||||||||||||||||||||
CAGTHIOGN_CDS2 MAGFSKVIATIFLMMMLVFATDMMAEAKICEALSGNFKGLCLSSRDCGNVCRREGFT

     CAGT_CDS1 DGSCIGFRLQCFCTKPCA
                | | || |.||| || |
CAGTHIOGN_CDS2 SGVCRGFPLKCFCRKPGA

Percentage ID = 88.00

Score = 790
Length of alignment = 80
Sequence GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence AF112443_CDS1 :  1 - 84 (Sequence length = 84)

GMU12150_CDS1 MSRSVPLVSTICVLLLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVC-R
              |.||. ... . . . |.||  . |     |   |   .   |  | ||  |  .|  
AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQG----KEI-CCKELTKPVK--CSSDPLCQKLCME

GMU12150_CDS1 TERFTGGHCRGFRRRCFCTKHC
               |.. .|||  .  .|.| |.|
AF112443_CDS1 KEKYEDGHCFTILSKCLCMKRC

Percentage ID = 28.75

Score = 1390
Length of alignment = 80
Sequence GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence AF128239_CDS1 :  1 - 107 (Sequence length = 107)

GMU12150_CDS1 MSRSVPLVSTICVLLLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVC-R
              |.||. ... . . . |.||  . |   .     | . | .||| |..|..|  || .
AF128239_CDS1 MARSIYFMAFLVLAVTLFVANGVQGQNNI-----CKTTSKHFKGLCFADSKCRKVCIQ

GMU12150_CDS1 TERFTGGHCRGFRRRCFCTKHC
               ..| .|||  ..|.|.|||.|
AF128239_CDS1 EDKFEDGHCSKLQRKCLCTKNC

Percentage ID = 33.75

Score = 100
Length of alignment = 65
Sequence GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)

GMU12150_CDS1 LLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVCRTERFTGGHCRGFRRR
              .   |   ..|  |..     |.   . . || |. . .  |  .|   ..|   ...
BOAJ5280_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQ-EPDKTCEVNR-CKANCVKKHKK

GMU12150_CDS1 CFCTKHC
               .    |
BOAJ5280_CDS1 ILAFTSC

Percentage ID = 16.92

Score = 100
Length of alignment = 65
Sequence GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)

GMU12150_CDS1 LLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVCRTERFTGGHCRGFRRR
              .   |   ..|  |..     |.   . . || |. . .  |  .|   ..|   ...
BOAJ5281_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQ-EPDKTCEVNR-CKANCVKKHKK

GMU12150_CDS1 CFCTKHC
               .    |
BOAJ5281_CDS1 ILAFTSC

Percentage ID = 16.92

Score = 2690
Length of alignment = 79
Sequence  GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)

 GMU12150_CDS1 MSRSVPLVSTICVLLLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVCR
               |.    ...|| ....|. ||      ||||||||||||||||| |.| .||||||.
CAGTHIOGN_CDS1 MAGFSKVIATIFLMMMLVFAT-----GMVAEARTCESQSHRFKGLCFSKSNCGSVCH

 GMU12150_CDS1 TERFTGGHCRGFRRRCFCTKHC
               || | ||||||||||||||.||
CAGTHIOGN_CDS1 TEGFNGGHCRGFRRRCFCTRHC

Percentage ID = 63.29

Score = 1800
Length of alignment = 79
Sequence  GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)

 GMU12150_CDS1 MSRSVPLVSTICVLLLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVCR
               |.    ...|| ....|. ||.||     |||. ||. |  ||| |||  .||.|||
CAGTHIOGN_CDS2 MAGFSKVIATIFLMMMLVFATDMM-----AEAKICEALSGNFKGLCLSSRDCGNVCR

 GMU12150_CDS1 TERFTGGHCRGFRRRCFCTKHC
                | ||.| ||||  .||| |  
CAGTHIOGN_CDS2 REGFTSGVCRGFPLKCFCRKPG

Percentage ID = 46.84

Score = 2000
Length of alignment = 79
Sequence GMU12150_CDS1 :  1 - 79 (Sequence length = 79)
Sequence     CAGT_CDS1 :  1 - 75 (Sequence length = 75)

GMU12150_CDS1 MSRSVPLVSTICVLLLLLVATEMMGPTMVAEARTCESQSHRFKGPCLSDTNCGSVCRT
              |.    .|.|| ...||. ||.||     |||. ||. |  ||| |||  .||.||| 
    CAGT_CDS1 MAGFSKVVATIFLMMLLVFATDMM-----AEAKICEALSGNFKGLCLSSRDCGNVCRR

GMU12150_CDS1 ERFTGGHCRGFRRRCFCTKHC
              | ||.| | ||| .||||| |
    CAGT_CDS1 EGFTDGSCIGFRLQCFCTKPC

Percentage ID = 51.90

Score = 110
Length of alignment = 32
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence  AF112443_CDS1 :  1 - 84 (Sequence length = 84)

ZMA133530_CDS1 CSASRCHLGCIHRGYKGTGSY-CRGRDCCCKH
                . |   .. .  .     .|  .|.. |||.
 AF112443_CDS1 MARSIYFMAFLVLAMTLFVAYGVQGKEICCKE

Percentage ID = 18.75

Score = 40
Length of alignment = 77
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence  AF128239_CDS1 :  1 - 107 (Sequence length = 107)

ZMA133530_CDS1 MAAVMCLVLATMSSTSPSFCQAGGCIGCPRAPPPPSDETCYEDLKCSASRCHLGCIH
               ||  . ..   . .   ..  | |  |        | .  . .|  . |.|.  ||.
 AF128239_CDS1 MARSIYFMAFLVLAV--TLFVANGVQGQNNICKTTSKH--FKGLCFADSKCRKVCIQ

ZMA133530_CDS1 RGYKGTGSYCRG-RDCCCKH
                .    |   .  | | |  
 AF128239_CDS1 EDKFEDGHCSKLQRKCLCTK

Percentage ID = 19.48

Score = 140
Length of alignment = 80
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence  BOAJ5280_CDS1 :  1 - 81 (Sequence length = 81)

ZMA133530_CDS1 AVMCLVLATMSSTSPSFCQAGGCIGCPRAPPPPSDETCYEDLKCSASRCHLGCI--H
                   . |. ..    .    |  .   .  |  |.|    |  |  .||   |.  |
 BOAJ5280_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQE---PDKTCEVNRCKANCVKKH

ZMA133530_CDS1 RGYK-GTGSYC--RGRD-CCCKH
               .     |.      |   | |. 
 BOAJ5280_CDS1 KKILAFTSCIKENNGNMYCRCQY

Percentage ID = 18.75

Score = 140
Length of alignment = 80
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence  BOAJ5281_CDS1 :  1 - 81 (Sequence length = 81)

ZMA133530_CDS1 AVMCLVLATMSSTSPSFCQAGGCIGCPRAPPPPSDETCYEDLKCSASRCHLGCI--H
                   . |. ..    .    |  .   .  |  |.|    |  |  .||   |.  |
 BOAJ5281_CDS1 MKNTVKLSLIGFVMLTVLLLGETVIAQKRKPCYSQE---PDKTCEVNRCKANCVKKH

ZMA133530_CDS1 RGYK-GTGSYC--RGRD-CCCKH
               .     |.      |   | |. 
 BOAJ5281_CDS1 KKILAFTSCIKENNGNMYCRCQY

Percentage ID = 18.75

Score = 300
Length of alignment = 75
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence CAGTHIOGN_CDS1 :  1 - 74 (Sequence length = 74)

ZMA133530_CDS1 AAVMCLVLATMSSTSPSFCQAGGCIGCPRAPPPPSDETCYEDLKCSASRCHLGCIHR
                |    |.||.      .  | | .    |    |.   . .|  | | |   |   
CAGTHIOGN_CDS1 MAGFSKVIATI-FLMMMLVFATG-MVA-EARTCESQSHRFKGLCFSKSNCGSVCHTE

ZMA133530_CDS1 GYKGTGSYCRGRDCCCKH
               |.   |. |||    |  
CAGTHIOGN_CDS1 GF--NGGHCRGFRRRCFC

Percentage ID = 25.33

Score = 110
Length of alignment = 83
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence CAGTHIOGN_CDS2 :  1 - 75 (Sequence length = 75)

ZMA133530_CDS1 MRIVYMAAVMCLVLATMSSTSPSFCQAGGCIGCPRAPPPPSDETCYEDLKCSASRCH
                 |  .  .| ||.||   . . .|.|                  . .|  |.  | 
CAGTHIOGN_CDS2 KVIATIFLMMMLVFATDMMAEAKICEA--------------LSGNFKGLCLSSRDCG

ZMA133530_CDS1 LGCIHRGYKGTGSYCRG--RDCCCKH
                 | . |.  |.. |||    | |. 
CAGTHIOGN_CDS2 NVCRREGF--TSGVCRGFPLKCFCRK

Percentage ID = 22.89

Score = 70
Length of alignment = 12
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence      CAGT_CDS1 :  1 - 75 (Sequence length = 75)

ZMA133530_CDS1 MRIVYMAAVMCL
                |.    .  | 
     CAGT_CDS1 FRLQCFCTKPCA

Percentage ID = 16.67

Score = 420
Length of alignment = 84
Sequence ZMA133530_CDS1 :  1 - 81 (Sequence length = 81)
Sequence  GMU12150_CDS1 :  1 - 79 (Sequence length = 79)

ZMA133530_CDS1 MRIVYMAAVMCLVLATMSSTSPSFCQAGGCIGCPRAPPPPSDETCYEDLKCSASRCH
                | | . . .|..|  . .|     .  |    . |    |.   . .   | . | 
 GMU12150_CDS1 SRSVPLVSTICVLLLLLVAT-----EMMGPTMVAEARTCESQSHRFKGPCLSDTNC-

ZMA133530_CDS1 LGCIHRGYKGTGSYCRG--RDCCC-KH
                | . |  . ||. |||  | | | ||
 GMU12150_CDS1 -GSVCRTERFTGGHCRGFRRRCFCTKH

Percentage ID = 26.19

Pairwise alignment scaled similarity score matrix

0 AF112443_CDS1 
1 AF128239_CDS1 
2 BOAJ5280_CDS1 
3 BOAJ5281_CDS1 
4 CAGTHIOGN_CDS1 
5 CAGTHIOGN_CDS2 
6 CAGT_CDS1 
7 GMU12150_CDS1 
8 ZMA133530_CDS1 


  0.059  0.003  0.002  0.003  0.002  0.137  0.023  0.040  0.002  0.002  0.016  0.028  0.002  0.002  0.087  0.022  0.034  0.005  0.005  0.091  0.117  0.024  0.037  0.003  0.003  0.088  0.058  0.065  0.003  0.001  0.004  0.004  0.010  0.004  0.002  0.013

Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/public_html/tutorials/bioLegato/multalign/bio7856454386989071696.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/public_html/tutorials/bioLegato/multalign/bio3291257679205033973.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/public_html/tutorials/bioLegato/multalign/bio28188473674222890.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_22
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

../gtk-2.0-key/gtkrc:10: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:18: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:29: Binding specification is unsupported, ignoring
../gtk-2.0-key/gtkrc:31: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:32: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:33: Binding assignment is unsupported, ignoring
../gtk-2.0-key/gtkrc:34: Binding assignment is unsupported, ignoring
Opening file: /home/psgendb/public_html/tutorials/bioLegato/multalign/bio6609252623185172009.tmp.fsa
INFO - Not enabling Google Tracking.
Java version: 1.5.0_24
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

/usr/share/themes/LighthouseBlue/gtk-2.0/gtkrc:53: Engine "lighthouseblue" is unsupported, ignoring
INFO - Initialising googletracker for usage stats.
java.lang.NullPointerException
	at javax.swing.JComponent._paintImmediately(JComponent.java:4848)
	at javax.swing.JComponent.paintImmediately(JComponent.java:4669)
	at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:451)
	at javax.swing.SystemEventQueueUtilities$ComponentWorkRequest.run(SystemEventQueueUtilities.java:110)
	at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209)
	at java.awt.EventQueue.dispatchEvent(EventQueue.java:461)
	at java.awt.EventDispatchThread.pumpOneEventForHierarchy(EventDispatchThread.java:242)
	at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:163)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:157)
	at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:149)
	at java.awt.EventDispatchThread.run(EventDispatchThread.java:110)
In paintImmediately null graphics
(C) 2003-2007 Jmol Development
Jmol Version 11.0.2  2007-04-24 19:38
java.vendor:Sun Microsystems Inc.
java.version:1.5.0_24
os.name:SunOS


FileManager.openFile(/var/tmp/jalview_pdb8097687117754434242.txt,0,0,0,0)
FileManager opening /var/tmp/jalview_pdb8097687117754434242.txt
SmarterJmolAdapter:The Resolver thinks:Pdb
SmarterJmolAdapter:het: FES
SmarterJmolAdapter:hetero: FES FE2/S2 (INORGANIC) CLUSTER
SmarterJmolAdapter:setunitcellitem 6 0.032257996
SmarterJmolAdapter:setunitcellitem 7 0.0
SmarterJmolAdapter:setunitcellitem 8 0.0
SmarterJmolAdapter:setunitcellitem 9 0.0
SmarterJmolAdapter:setunitcellitem 10 0.0
SmarterJmolAdapter:setunitcellitem 11 0.025523
SmarterJmolAdapter:setunitcellitem 12 0.0
SmarterJmolAdapter:setunitcellitem 13 0.0
SmarterJmolAdapter:setunitcellitem 14 0.0
SmarterJmolAdapter:setunitcellitem 15 0.0
SmarterJmolAdapter:setunitcellitem 16 0.011973
SmarterJmolAdapter:setunitcellitem 17 0.0
openFile(/var/tmp/jalview_pdb8097687117754434242.txt,0,0,0,0)197 ms
frame: haveSymmetry:false haveUnitcells:true haveFractionalCoord:false
1 model in this collection. Use getProperty "modelInfo" or getProperty "auxiliaryInfo" to inspect them.
measurement[0] = [2, 734, 664, 1.328 nm]
Java version: 1.6.0_23
x86 SunOS 5.10
Jalview Version: 2.4.0.b2
# INFO: Setting default net timeout to 30 seconds.
Java Accessibility Bridge for GNOME loaded.

Opening file: /home/plants/frist/tutorials/defensin/bio7780552517543492078.tmp.fsa
INFO - Initialising googletracker for usage stats.
