I might be wrong, but I get the feeling this is more of a biology thing for you than it is a Perl thing, so I'm helping out more than I usually do. Please make sure you understand the code below (and its limitations) before you use it.

Good luck.

use strict;
use warnings;

# Read the first 7 lines of metadata.
# Assuming there are always 7 lines of metadata.
foreach (1..7)
    {
    # Read a line of data.
    my $header_data = <DATA>;
    
    # Remove the end of line character.
    chomp $header_data;

    # Split the string into 2 parts, using white space as a separator.
    my ($lable, $string) = split /\s+/, $header_data, 2;

    # only pay attention to the "Motif" line.
    next if ($lable ne 'Motif');
    print "$string ";
    }    

# Process the next 10 lines of data.
# Assuming there are always 10 lines of data.
foreach (1..10)
    {
    # Declare a variable to hold the data in the file.
    my %base_pairs;

    # Read a line of data.
    my $line = <DATA>;

    # Remove the end of line character.
    chomp $line;

    # Split the string into 5 parts, using whitespace as a separator.
    # Assuming the Position is always in the same order in the file.
    (undef, $base_pairs{A}, $base_pairs{C}, $base_pairs{G}, $base_pair
+s{T}) = split /\s+/, $line, 5;
    my @letters = keys %base_pairs;

    # Start with the first column value and make it the max. value.
    my $max = pop @letters;

    # Compare each value to the maximum.
    foreach my $letter (@letters)
        {
        # What if two (or more) values are equal???
        if ($base_pairs{$max} < $base_pairs{$letter})
            {
            # The current value was grater than the maximum, so make i
+t the new maximum.
            $max = $letter;
            }
        }
    # Print the letter representing the maximum value.
    print $max;
    }
# print an end of line character.
print "\n";

__DATA__
TF    Unknown
TF Name    Unknown
Gene     ENSG00000113916
Motif     ENSG00000113916___1|2x3
Family    C2H2 ZF
Species    Homo_sapiens
Pos    A    C    G    T
1    0.538498    0.157305    0.157633    0.146564
2    0.072844    0.008771    0.877166    0.0412175
3    0.959269    0.013107    0.015961    0.0116621
4    0.852439    0.023883    0.016813    0.106864
5    0.57332    0.068801    0.181385    0.176494
6    0.139513    0.074798    0.737607    0.0480813
7    0.735484    0.091299    0.09091    0.0823067
8    0.79932    0.027041    0.137306    0.0363319
9    0.16103    0.12536    0.109938    0.603672
10    0.622356    0.06782    0.115463    0.194361
[download]

Cheers,

Brent