yeah, i tried with use warnings and use strict, here is the program which i tried.

#!/usr/bin/perl 
use strict; 
use warnings; 
open(FH1,"read.txt"); 
open(FH2,"qual.txt"); 
my @arr1=<FH1>; 
my @arr2=<FH2>; 
my $joi1=join(' ',@arr1); 
my $joi2=join(' ',@arr2); 
my @new=split('>',$joi1); 
my @numbers=split('>',$joi2); 
my @new; 
my @seqid; 
foreach(@new){         
my($seq_id,$seq)=split(/\n/,$_);         
push(@alp,split(' ',$seq));         
push(@seqid,$seq_id); } 
my @numbers; 
my @numid; 
foreach(@numbers){         
my ($num_id,$numb)=split(/\n/,$_);         push(@num,split(' ',$numb))
+;     
push(@numid,$num_id) 
} 
my @keep= grep {$_ < 1 || $num[$_]>=10 || $alp[$_-1] ne $alp[$_-0]} 0.
+.$#num; 
print (join(' ',@alp[@keep]),"\n"); 
print (join(' ',@num[@keep]),"\n");
[download]

the result which i got is

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
[download]

Is this problem because i am using more than one string from 2 different files? in the above program, why are we not comparing the character repetition at all? In some cases, if the number is less than 10, but doesnt come into repeted continous characters, it should be removed. Please suggest what can be done. I am not very good at perl :-( Thanks

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