Hi @All,

short version:
Is it possible to specify more arguments in "Full parameter list"-mode, 
particularly those that're implicitely described in YASRA-mode (match/mismatch 
rewards and step-size (Z/step))?

long version:
I'm dealing with 454 reads and it's crucial to the scenario to have the 5' ends 
aligned properly (in terms of sensitivity), so all the YASRA-templates 
comprising heavy gap penalties perform fairly poor as soon as there's a gap 
nearby the 5' end. However, heading to "Full parameter list"-mode leads to 
excessive CPU-use, because (presumably) the step-size (default=1?) is left 
unset. Also, it'd be great to be able to alter not only gap penalties, but 
match/mismatch rewards as well. (Obviously a mismatch would cause the same 
problem).

Examples:
AAAAAAAAAA (target)
AAAAATAAAA (query)

=> I need the alignment boundary to be found at position 1, rather than behind 
the mismatched T and this cleary doesn't work as long as the mismatch penalty 
is too large (same applies for gap-open/extend penalties).

Thanks in advance and Cheers,
Uwe
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