* What's about "align_to_scf" ?

  This is important if you want to see the real traces within the contig editor from STADEN at a given position.

  Note: there are no information given within the ACE assembly to recalculate the trace position backward from assembly.
  STADEN "trev" will access/open traces as given from "sequencer machine" and Roche assembly give you only the complete assembly
  information. This is the problem !

  Are you firm with gap4 ?
  The program "trev" is automatically called within "gap4".
  And you start this with:
  -> open gap4 database
  --> open contig editor, select contig
  ---> double-click on one letter will open this trace at this position and set cursor to exact this position !
       double-click on the consensus line will open all traces at this position !

  You can also see the "slack" by enable/disable "show cutoff";

  Example ?
  Try this very simple test data and verify this letter by letter:


  % align_to_scf -f test.qry -o test.aln

  --- test.qry ---
  >F0FH8BE01EUM6Y              <- name of read from sff archive
  ATGCATCATG-ATGC              <- fasta sequence of this read from ace file
  ATGCATGCATGCATGC             <- fasta sequence of this read from sff trace file


  And you should get this output "test.aln" ( see also CAF format description ) :

  >F0FH8BE01EUM6Y
  Align_to_SCF 1 6 1 6
  Align_to_SCF 7 10 8 11
  Align_to_SCF 12 15 13 16