Thanks Choroba for the suggestions.

I am checking a rule against a string of sequence (19 letter longs) in a while loop and formed this filter

So basically, I want to match A at position 3, T at position 10, [ACT] at position 13, [AT] at position 19 and atleast 3 A's or 3 T's from position 15-19 and the $gcper should be in between 30-52.

if (($seq =~/\w{2}A\w{6}T\w{2}[ACT]\w[GCA{4}T{4}]{4}[AT]/) 
   && ($gcper >= 30 && $gcper <= 52))
     {
    print "$seq\t$seqpos\t$gcper\n";
     }

[download]

I checked the result and it seemed to work, i need help in wheather this code writing is ok or i can improve it better.

Another thing which I want to check is: no GC stretch more than 9 letters long, but I don't know how I can insert that check in the above code. 

GCAGGTGGATCTATTTCAT    3201-3220    42.11
TAAGAGGTGTTATTTGGAA    3268-3287    31.58
ATACGATGCTTCAAGAGAA    3346-3365    36.84
CAAGCTCATCATACTGGCT    1201-1220    47.37
GGTACTGACTTTGCTTGCT    2923-2942    47.37
CGTAGTGTTAAGTTATAGT    3003-3022    31.58
GTATGGGTAGGGTAAATCA    3248-3267    42.11
CCTGCTGTGATACGATGCT    3337-3356    52.63
CCTGCGCGCGCGCGATGCT    3300-3318    50.63

[download]

In reply to Re^6: Filter and writing error log file by newtoperlprog
in thread Filter and writing error log file by newtoperlprog

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