There is a neat trick for finding difference between similar equal length ASCII strings: xor them together and any non-zero bytes are different. Consider:

use strict;
use warnings;

my $one= "AGCTGATCGAGCTAGTACCCTAGCTC";
my $two= "AGCTGATCGAGCTAGTACCCTATCTC";
my $diff = $one ^ $two;

$diff =~ tr/\0/x/c;

my $start = -1;

while (-1 < ($start = index $diff, 'x', ++$start)) {
    print "Difference at $start\n";
}

[download]

Prints:

Difference at 22

[download]

The tr/// changes non-zero bytes to x. The while loop then uses index to search through the difference string for the x bytes and reports their index (0 based position).

Perl reduces RSI - it saves typing

In reply to Re: match and mismatch by GrandFather
in thread match and mismatch by heidi

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