substr( $string, -5, 5 ) = '';

##</code><code>##

use strict;
use warnings;
use Data::Dumper;

my @lines = <DATA>; # assume groups of four lines
chomp( @lines );
my $n = 5;          # to be cut off
for( my $i=0; $i<@lines; $i+=4 ) {
		substr( $lines[$i+1], -$n, $n ) = '';
		substr( $lines[$i+3], -$n, $n ) = '';
}
print Dumper( \@lines );

__DATA__
@HWI-ST1023:184:C1V8LACXX:7:1101:1142:2247 2:N:0:TGACCA
GTAGGGGCTGCGCGAACGCAAACCCCCGCTGCCACAAATGATCGTCGGACTGTAGAACTCTGAACGTGTAGATCTCGGTGGCCGCCGTATCATTAAAAAAA
+
?1=DBB@DCFFFFIGIIII6DGHHIII6@=AEEDDEEC;@C>@?(;;B;@B?9BCDAA3>(:@@CB+8(9>@:@CCBB289(259@B9B8?A:@C@>CC@B
@HWI-ST1023:184:C1V8LACXX:7:1101:1450:2022 2:N:0:TGACCA
ACGTGCCCTCGGCCAGAAGGCTTGGGGCGCAACTTGCGTTCAAAGACTCGATGGTTCACGGGATTCTGCAATTCACACCAAGTATCGCATTTCGCTACGTT
+
?@@DDDFFADFFHIJIIFG>FHIJJJJJGIIBH=DHGHHDDFFF;AEAC?=>CD-:@CDBDBDBDD>CDDD:ACDCDDDDD?(4>CBBD?@DDDDDDDD8?
@HWI-ST1023:184:C1V8LACXX:7:1101:1457:2047 2:N:0:TGACCA
GCGTCGCCAGCACAGAGGCCATGCGATCCGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCGCGTCGACCTTTTATCTAATAAATGCGTCCCT
+
@CCDFFFFGHHHHJIIIJJIJJJJIIJJJJFHIBFBFHIGJJIGI@GHGGEHHHHHHFFDDABDDDDDDDDDDDBDBBBDCCCCCDDDDCDDEECB8<@DD