ClustalW 1.7 Multiple Sequence Alignment Parameters

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DNA Sequence Parameters:

Fast Pairwise Alignment Parameters:
   K-tuple (word) size: 2
   Window size: 4
   Scoring method: percentage
   Number of top diagonals: 4
   Gap penalty: 5

Multiple Alignment Parameters:
   Gap opening penalty: 10.0
   Gap extension penalty: 5.0
   Weight transitions: Yes

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Protein Sequence Parameters:

Fast Pairwise Alignment Parameters:
   K-tuple (word) size: 1
   Window size: 5
   Scoring method: percentage
   Number of top diagonals: 5
   Gap penalty: 3

Multiple Alignment Parameters:
   Weight matrix: blosum
   Gap opening penalty: 10.0
   Gap extension penalty: 0.05
   Hydrophilic gaps: On
   Hydrophilic residues: GPSNDQERK
   Residue-specific gap penalties: On

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Other Parameters:
   Quicktree (always On): On
   Divergence cutoff (% identity for delay): 40
   Gap separation distance: 8
   End gap separation penalty: Off
   Output order: aligned

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Last change: Tue Aug 12 12:19:23 CDT 1997