Here is some code to show you perl idioms on how to approach this problem.

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

my ($infile1 ,$infile2) = @ARGV;

open (my $in1 ,"<", $infile1) or die "Cannot open '$infile1':$!\n";
open (my $in2, "<", $infile2) or die "Cannot open '$infile2':$!\n";
my @values;
while ( <$in1> ){
  chomp;
  my @one = split;
  next unless scalar(@one) >= 3; # Must have at least 3 
  push @values, [@one[0..2]];
}
close $in1;

while (<$in2>){
    chomp;
    my @two = split;
    next unless scalar(@two) >= 5; # Must have at least 5
    next unless grep { 
               $_->[0] eq $two[0]  
           and $_->[1] eq $two[3]
           and $_->[3] eq $two[4]
      } @values;
    print join("\t",@two[0,3,4]) , "\n"
}
close $in2;
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You will need to understand "array slices", and references.