#!/usr/bin/perl -w
use strict;
use Data::Dumper;

my $fseq =  'CCCCGCGC';
my $nsub =  ['CCCCG',
              'CCCGC',
                'CGCGC', ];

my $result =['C----',      # this is not a parameter but 
              '----C',     # intended result obtained with Dumper
                '---GC' ];


my @result = remove_overlap($fseq,$nsub);
print Dumper \@result;

# I'm not so sure how to approach
# this problem with the subroutine below
sub remove_overlap
{
    my  ($fseq,$nsub)   = @_;
    my  @result;
    my  $slen = length $nsub->[0];

    foreach  (@{$nsub})
    {
       # ????
       my $pos = index($fseq,$_);
       print "$pos\n";
    }
    return @result;
}

#---------- The other instances of the problem
#---------- with the intended $result

my $fseq2 =    'CGTGGCGC';
my $nsub2 =  [  'GTGGC',
                 'TGGCG'];
my $result2 =[  'G----',       # intended result
                 '----G'];

my $fseq3 =   'CCGCGCTC';
my $nsub3 =  [ 'CCGCG',
                'CGCGC',
                 'GCGCT',
                  'CGCTC'];
my $result3 = ['C----',      # intended result
                '----C',
                 '----T',
                  '----C'];

# No overlapping case
my $fseq4 =   'AAGCTATA';
my $nsub4 = [ 'AAGC',
                  'TATA'];
my $result4 = ['AAGC','TATA']; # intended result