So you have three arrays, each of which is a unique list of numbers, and you want to construct @locations as a list of where they came from, in order. You also construct @new_gp, which looks like it should be the pairs list flattened out.

When you need to look up a mapping, like a number mapped to its source, use a hash.

use strict;
use warnings;

# Just generating data here.
my @rep1 = (1..5);
my @rep2 = (6..10);
my @rep3 = (11..15);

my @pairs = map {sprintf "%d %d", int(rand(15)+1), int(rand(15)+1)} 1.
+.10;

# Here's the magic, fairly information-dense.
# Make a list of name-array associations, pass it to map
# Then go through the members of the array and associate each member
# with the name.
my %sources = map {
    my ($name, $ref) = @$_;
    map {($_ => $name)} @$ref;
} ([rep1 => \@rep1], [rep2 => \@rep2], [rep3 => \@rep3]);

# Now, when you have a number $n1, its source is $sources{$n1}
my (@locations, @new_gp);
for (@pairs) {
    print "$_: ";
    my ($n1, $n2) = split;
    push @new_gp, $n1, $n2;
    push @locations, @sources{$n1, $n2};
    print "$n1 came from $sources{$n1}; $n2 came from $sources{$n2}\n"
+;
}
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