File looks like this:
99_999_852_F3	chr9	97768833	97768867	ATTTTCTTCAATTACATTTCCAATGCTATCCCAAA	+	35
99_999_852_F3	chr9	97885645	97885679	ATTTTCTTCAaTTACATTTCCAATGCTATCCCAAA	+	35
99_99_994_F3	chr10	47028821	47028855	AGACAAAAAGGCCATCAACAGATCAGTAAAGGATC	+	35
...

##</code><code>##

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

open (INFILE, "inputfile.txt") or die $!;
open (OUTFILE, '>', "sorted.txt") or die $!;

foreach (sort <INFILE>){
	print OUTFILE $_;
}

close(OUTFILE);
close(INFILE);
exit;