[EMBOSS] Help with stretcher

[michael watson (IAH-C)]

Hi

I am using stretcher from emboss in a perl script.  I am trying to
globally align a relatively short sequence with quite a long one.
Basically, the short one sits bang in the middle of the long one, with
almost 100% identity.  However, no matter how much I play with the
gaplength and gappenalty options, stretcher insists that the the first
base of the short sequence aligns with the first base of the long
sequence, followed by a HUGE gap in the alignment, followed by the rest
of the sequences, correctly aligned.  It's doing my nut in.

I'm using EMBOSS 2.9.0 on Suse Linux.

Any help?

Mick