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Basic Wconsensus

• The number of standard deviations (-s):

• Queue Size : (max number of matrices to save between cycles, -q):

• Override observed frequencies with prior probabilities (-d)?

• Sequence Alphabet and Normalization Information (-A):

• Autoset (-A) option above :
Choose an alphabet DNA Protein

• Alphabet is Case Sensitive (-CS)?

• Complement option (-cn):
0 - ignore the complement 1 - include both strands as separate sequences 2 - include both strands as a single sequence 3 - assume pattern is symmetrical

• Linear search method (-l ) ?

• Contribute zero or more words per
  matrix and repeat matrix building
  cycle a maximum of (-n ):

• Contribute one or more words per
  matrix and repeat matrix building
  cycle a maximum of (-N ):

• Minimum distance between the
  starting points of words within
  the same matrix pattern (-m ):

• Terminate this many cycles after the current most significant alignment
  is identified (-t ):

• Top Progeny Matrices (-prn ):
1 - save regardless of parentage 2 - try to save for each parental matrix

• Terminal Gaps (-pgn ):
0 - do not permit terminal gaps 1 - permit penalized terminal gaps

• Number of top matrices to print from each cycle (-pt ):

• Number of matrices to print from the final cycle (-pf ):