Wow .... I never thought I'd get this much help this fast. Thankyou both very much.
"(Note that it is assumed that $#query_sequence = $#subj_sequence)"
The problem is that they aren't equal - it's a bioinformaticological alignment problem - so I have 2 sequences, each with an alignment start and end position, which aren't necessarily at the start and end of the sequence.
Poj's thing seems to work - thankyou.
Marinegirl x
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