The most common and most likely answer to this crossword clue is the 5 plus 4 letter word TENOR CLEF
I've seen this crossword clue in The Guardian
T
E
N
O
R
C
L
E
F
Buddy explains!
The straight part
We know that "Mark alongside notes/Mark alongside notes" is the straight/definition part of the clue. The straight part is often a synonym or definition, in this case mark alongside notes/mark alongside notes = tenor clef.The cryptic/wordplay part
In cryptic crossword there's often an wordplay/cryptic part as well.This part involves a more complex hint, such as an anagram, homophone, hidden word, etc.
Sadly, We don't have an explanation for this specific crossword clue yet.