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Well, I'm sure you can find a more efficient approach, but here's a simplistic solution using standard UNIX tools: zcat file.fastq.gz | grep CGC | awk -F'CGC' 'NR%4==2{a[NF-1]++}END{for(i in a){print i,a[i]}}' | sort -rnk2 I tested this on a 2.6G fastq file (exome data) and it took: real 1m18.987s user 1m41.392s sys 0m10.684s ...

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