big peak at maximum sequencing length

[First citizen of GWIPS]

I presume you sequenced libraries with 50SE kits in which case what you see as 51 likely correspond to RNA fragments longer than 50. If you were doing size selection for ~30 fragments there should be no such fragments. If it is not a unique sequence, but something that aligns to different locations, Id' still try to better understand its nature. If you analyze the distribution of the fragments across different functional regions of mRNAs, i.e. leader/CDS/trailer what the distribution would look like? Like RNA-seq control or ribo-seq?
Yours,
PurpleUnamiBeans