$seq =~ s/
    (\d+):(\d+):(\d+)

    (?:;|\s)*

    (\1):(\2):(?{1+($3|$6)})

    /$1:$2:$3-$6/xg;
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FWIW, the (?{1+($3|$6)}) expression | embedded code expression in the quoted regex just adds 1 to the bitwise-or of $3 and $6 (treated as numbers... I think) and then throws away the result; it's a no-op.