Hi rnahi,
Thanks so much for your answers. Your solutions provide the correct result but also more. 
my $fseq1= 'CCCCGCGC';
my @nsub1= ('CCCCG', 
             'CCCGC', 
               'CGCGC');

#produces

$result1 = [
            [ 0, 'C----' ],
            [ 1, '----C' ],
            [ 1, 'CC---' ],   # but this is extra
            [ 2, '---GC' ]
          ];

[download]
And this 
my $fseq2=   'CCGCGCTC';
my @nsub2= ( 'CCGCG',
              'CGCGC',
               'GCGCT',
                'CGCTC' );

#produces

$result2 = [
            [ 0,'C----' ],
            [ 1,'----C' ],
            [ 1,'C----' ], # extra
            [ 2,'----T' ],
            [ 2,'G----' ], # extra
            [ 3,'----C' ],
           ];

[download]


How can I modify your code such that it simply gives: 


# So here we can observe that every element of the 
# array is only produced 'once'

# E.g (0,1,2) versus (0,1,1,2) 

$result1 = [
            [ 0, 'C----' ],
            [ 1, '----C' ],
            [ 2, '---GC' ]
          ];

# E.g (0,1,2,3) versus (0,1,1,2,2,3) 
$result2 = [
            [ 0,'C----' ],
            [ 1,'----C' ],
            [ 2,'----T' ],
            [ 3,'----C' ],
           ];

[download]
Regards,
Edward

In reply to Re^2: Identifying Overlapping Area in a Set of Strings by monkfan
in thread Identifying Overlapping Area in a Set of Strings by monkfan

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