#!/usr/bin/perl 
use strict;
use warnings;

my $ctfile = "M23263_rna_300-1.dat_1.ct";
my $matchfile = "match_super.dat";

my @match;my %hash;my $fragment; my $position;
open (A, "<", $matchfile) or die "Check the file $!\n";
while (my $line = <A>)
{
    chomp $line;
    (my $mat, $fragment, my $score, $position) = split(/\t/, $line);
    $hash{$fragment} = $position;
}

foreach my $key(keys %hash)
{
#    print "$key\t$hash{$key}\n";
    my @temp = split ("", $key);
    foreach my $val(@temp)
    {
	print "$val\t$hash{$key}\n";
    }
}
close (A);

my ($num1, $base, $num2, $num3, $connect, $num4);
open (B, "<", $ctfile) or die "Check the file $!\n";
while (my $ctline = <B>)
{
    chomp $ctline;
    if ($ctline =~ /^(\d+\s+dG.*)/)
    {
#	print "$1\n"; next;
	next;
    }
    my @tempfile = split (/\s+/, $ctline);
    my $base = $tempfile[1];
    my $connect = $tempfile[4];
    print "$base\t$connect\n";
}
close (B);