## Answers

#!/bin/bash #set first and second arguments (dnafile and base respectively) dir=$1 base=$2 count=$(grep -o ${base} ${dir} | wc -l) echo "${count}"

OUTPUT :

$ ./countmatches ttt dnafile 1

(Alternative awk script for the same )

AWK SCRIPT :-

grep -v ">" < input.fa | tr -d '\n' | sed 's/\([ATGCatgcNn]\{3,3\}\)/\1#/g' | tr "#" "\n" | awk '(length($1)==3)' | sort | uniq -c.

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