Not sure what you want, really, but to remove the last 5 chars from a $string, you can do

substr( $string, -5, 5 ) = '';
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UPDATE: I am still not sure what you want but it seems that there are groups of 4 lines and you want to shorten the second and fourth line of each group by 5 chars?

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
GTAGGGGCTGCGCGAACGCAAACCCCCGCTGCCACAAATGATCGTCGGACTGTAGAACTCTGAACGTGTA
+GATCTCGGTGGCCGCCGTATCATTAAAAAAA
+
?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
ACGTGCCCTCGGCCAGAAGGCTTGGGGCGCAACTTGCGTTCAAAGACTCGATGGTTCACGGGATTCTGCA
+ATTCACACCAAGTATCGCATTTCGCTACGTT
+
?@@DDDFFADFFHIJIIFG>FHIJJJJJGIIBH=DHGHHDDFFF;AEAC?=>CD-:@CDBDBDBDD>CDD
+D:ACDCDDDDD?(4>CBBD?@DDDDDDDD8?
@HWI-ST1023:184:C1V8LACXX:7:1101:1457:2047 2:N:0:TGACCA
GCGTCGCCAGCACAGAGGCCATGCGATCCGTCGAGTTATCATGAATCATCAGAGCAACGGGCAGAGCCCG
+CGTCGACCTTTTATCTAATAAATGCGTCCCT
+
@CCDFFFFGHHHHJIIIJJIJJJJIIJJJJFHIBFBFHIGJJIGI@GHGGEHHHHHHFFDDABDDDDDDD
+DDDDBDBBBDCCCCCDDDDCDDEECB8<@DD
[download]