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AGCT 0 370 1
AGAG 0 32 0
TGAA 2 233 0
AGGT 3 52 1

use strict;        # before anything else
...
print "after sorting...\n";
print Dumper @sorted;

before sorting...
$VAR1 = 'AGCT    0    370    1';
...
$VAR2 = 'AGCT    0    370    1';
$VAR3 = 'TGAA    2    233    0';
$VAR4 = 'AGGT    3    52    1';