If I understand you query correctly, a quick non perl solution is 
grep -A2 -f candseq_data_file rawseq_data_file

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A perlish way of checking the presence of a string in an array is 
@is_member = grep { $_ =~ /$candseq/} @rawseq;

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In reply to Re^3: Comparing strings with special characters by umasuresh
in thread Comparing strings with special characters by skolobs

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