Scaffold604	947743	947827 
Scaffold604	941827	941924 
Scaffold604	938360	938389 
Scaffold604	932556	933427 
Scaffold3712	176554	176704 
Scaffold3712	180811	180934 
Scaffold3712	181470	181554

 
27051543	Scaffold446353	19	1442 
27051545	Scaffold121539	7428	11547 
27051546	Scaffold121539	80165	98618 
27051547	Scaffold121539	167332	175700 
27051549	Scaffold267160	81607	82942 
27051550	Scaffold267160	79672	80108

 
while (<IN>) 
{ 
    chomp; 
    my @fields = split /\t/; 
    foreach my $PAC (sort keys %loci) 
    { 
	my ($scaf, $start, $stop) = @{$loci{$PAC}}; 
	my $min = ($start - 100); 
	my $max = ($stop + 100); 
	if ( ($scaf eq $fields[0]) && ($fields[1] > $min) && ($fields[2] < $max) ) 
	{ 
	    print "$scaf\t$fields[1]\t$fields[2]\n"; 
	} 
    } 
} 
close (IN);

#!/usr/bin/perl 
use strict; 
use warnings; 
 
my $f1 = <<EOF; 
Scaffold604	947743	947827 
Scaffold604	941827	941924 
Scaffold604	938360	938389 
Scaffold604	932556	933427 
Scaffold3712	176554	176704 
Scaffold3712	180811	180934 
Scaffold3712	181470	181554 
Scaffold446353	19	1400 
Scaffold121539	168000	175000 
EOF 
 
my $f2 = <<EOF;   
27051543	Scaffold446353	19	1442  
27051545	Scaffold121539	7428	11547 
27051546	Scaffold121539	80165	98618 
27051547	Scaffold121539	167332	175700 
27051549	Scaffold267160	81607	82942 
27051550	Scaffold267160	79672	80108 
EOF 
 
my %data; 
open my $fh2, '<', \$f2 or die $!; 
while (<$fh2>) { 
	chomp; 
	my (undef, $scaff, $start, $stop) = split /\t/; 
	push @{ $data{$scaff} }, {start => $start, stop => $stop}; 
} 
close $fh2 or die $!; 
 
open INSIDE, ">", 'inside.txt' or die $!; 
open OUTSIDE, ">", 'outside.txt' or die $!; 
 
open my $fh1, '<', \$f1 or die $!; 
while (<$fh1>) { 
	my ($scaff, $field1, $field2) = split /\t/; 
	if (my $aref = $data{$scaff}) { # array reference 
	 
		my (%seen_inside, %seen_outside); 
		 
		for my $href (@$aref) {     # hash reference 
			if ($href->{start} - 100 < $field1 && $field2 < $href->{stop} + 100) { 
				print INSIDE unless $seen_inside{$_}++; 
			} 
			else { 
				print OUTSIDE unless $seen_outside{$_}++; 
			} 
		} 
	} 
} 
close $fh1 or die $!; 
close INSIDE or die $!; 
close OUTSIDE or die $!;