Not sure about the else branch. If my assumption of printing the unchanged data is correct, then there are further simplifications possible. 

use strict;
use warnings;

my $threshold = 1000;

# being lazy:
my @file_array = map { [ split /\s+/ ] } <DATA>;

for( my $i=0; $i<@file_array-2; $i+=2 ) {
    if( $file_array[$i  ][3]-$file_array[$i+2][2] < $threshold and
        $file_array[$i+1][3]-$file_array[$i+3][2] < $threshold ) {
        print "$file_array[$i  ][0] $file_array[$i  ][2] $file_array[$
+i+2][3]\n"; 
        print "$file_array[$i+1][0] $file_array[$i+1][2] $file_array[$
+i+3][3]\n";
    } else {
        # not sure
        print "$file_array[$i  ][0] $file_array[$i  ][2] $file_array[$
+i  ][3]\n"; 
        print "$file_array[$i+1][0] $file_array[$i+1][2] $file_array[$
+i+1][3]\n";
    }
}
print "$file_array[-2][0] $file_array[-2][2] $file_array[-2][3]\n"; 
print "$file_array[-1][0] $file_array[-1][2] $file_array[-1][3]\n";

__DATA__
link1 myco1 16 13013 color=chr1
link1 myco2 7419028 7432025 color=chr1
link2 myco1 13016 31245 color=chr1
link2 myco2 7432026 7450255 color=chr1
link3 myco1 31569 50386 color=chr1
link3 myco2 7450876 7469693 color=chr1
link4 myco1 53241 82019 color=chr1
link4 myco2 7472518 7501295 color=chr1
link5 myco1 82667 85039 color=chr1
link5 myco2 7511397 7513769 color=chr1
link6 myco1 85052 162535 color=chr1
link6 myco2 7513770 7591243 color=chr1
link7 myco1 3519888 3527802 color=chr10
link7 myco2 6192981 6200895 color=chr10
link8 myco1 3531711 3535088 color=chr10
link8 myco2 6200982 6204356 color=chr10
link9 myco1 3537764 3568351 color=chr10
link9 myco2 6204393 6234981 color=chr10
link10 myco1 3585050 3670398 color=chr10
link10 myco2 6236328 6321680 color=chr10

[download]

In reply to Re^3: problem in for loop by hdb
in thread problem in for loop by MVRS

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