If you want a substring from character 5 through character 10 including both then the substring length will be 10 - 5 + 1. The substr function counts offsets from zero so if you are counting from one you need to make an adjustment. The following code assumes you are counting like substr

#
#                    1         2         3
#          01234567890123456789012345678901234
my $seq = "LPNTGVTNNAYMPLLGIIGLVTSFSLLGLXKARKD";

#
# Note that substr counts offsets from zero so adjust
# if you are counting from one.

my $start = 5;
my $end = 10;
my $length = $end - $start + 1;

my $cut = substr $seq, $start, $length;
print "$cut\n";
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this prints

VTNNAY
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Cheers,

JohnGG