while read r;do i= s=${r#*ATG} ((${#s}==${#r}))&&s= until [[ ${s:i:3} =~ (TAA|TAG|TGA) ]]||((i+3>${#s}));do ((i+=3));done echo ${s:0:i} done
Note that non-ascii characters in the above source code will be escaped (such as \x9f).
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