So you are using 1 based numbering and you need to do the following:

use strict;
use warnings;

my $seq= 'ABCDEFGHIJKLM';
my $start=5;
my $end=7;

print substr $seq, $start - 1, ($end - $start) + 1;

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Prints:

EFG

[download]
DWIM is Perl's answer to Gödel

In reply to Re^2: get substring when you know START and END??? by GrandFather
in thread get substring when you know START and END??? by Anonymous Monk

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