Hi,

What does the input file look like? Are any of these formats in the form that you have?

One problem I see is you are altering an array with pop while iterating over the array and this will likely cause problems.

Your code:

foreach $value (@num_value) 
            {
                if ($value<$cut_off)
                {     
                    pop(@num_value);                                  
+                  
                }else{
                    last;
                }    
            }
        $sub1=substr($dna,-@num_value); 
        
        @qscopy=reverse @num_value;
        
        foreach $value (@qscopy) 
            {
                if ($value<$cut_off)
                {
                    pop(@qscopy); 
                }else{
                    last;                            
                }
            }
[download]

First you iterate over @num_value popping off elements (wrongly I believe) and then you reverse the array into @gscopy and pop again, (wrongly again I believe), if the amount is less than $cut_off.