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#!/usr/bin/perl 
use strict; 
...
my @keep= grep {$_ < 1 || $num[$_]>=10 || $alp[$_-1] ne $alp[$_-0]} 0.
+.$#num; 
print (join(' ',@alp[@keep]),"\n"); 
print (join(' ',@num[@keep]),"\n");

Use of uninitialized value in split at sample.pl line 15,<FH2> line 6.
Use of uninitialized value in split at sample.pl line 21,<FH2> line 6.
Use of uninitialized value in string ne at sample.pl line 24, <FH2> li
+ne 6. 
Use of uninitialized value in join or string at sample.pl line 25, <FH
+2> line 6. 
TGACTTTTGCAAAGCTCGTA TGACTTTTGCAAAGCTCGTA TGACTTTTGCAAAGCTCGTA        
+                                            34 45 34 23 32 43 54 45 3
+4 12 23 45 54 65 34 23 54 42 34 45 34 23 32 43 54 45 34 12 23 45 54 6
+5 34 23 54 42 34 45 34 23 32 43 54 45 34 12 23 45 54 65 34 23 54 42