I'm a little confused by your problem but I'll offer the following advice anyways. If you simply want the last 1000 characters of a string the following should be sufficient: 
my $sub = substr($seq, -1000);

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Your substr doc should point out that negative positions work from the end of the string.

In reply to Re: why is substr behaving odd? by bschmer
in thread why is substr behaving odd? by usless_blonde

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