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' ],
           ];