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diff --git a/dundee-conf/settings/ClustalLimits.xml b/dundee-conf/settings/ClustalLimits.xml
new file mode 100644
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+++ b/dundee-conf/settings/ClustalLimits.xml
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+<?xml version="1.0" encoding="US-ASCII" standalone="yes"?>
+<limits>
+ <runnerClassName>compbio.runner.clustal.ClustalW</runnerClassName>
+	<limit isDefault="false">
+		<preset>Disable gap weighting (Speed-oriented)</preset>
+		<seqNumber>2000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="true">
+		<seqNumber>1000</seqNumber>
+		<seqLength>1000</seqLength>
+	</limit>
+	<limit isDefault="false">
+		<preset># LocalEngineExecutionLimit #</preset>
+		<seqNumber>40</seqNumber>
+		<seqLength>500</seqLength>
+	</limit>
+</limits>