text: user9142: I have to manually curate some tRNA sequences in order to have their original sequence without modifications. I am getting these sequences from tRNAdb. In these sequences, I found often "_" symbols.
  They provide this list of symbols and "_" corresponds to insertion. My question is the insertion of what? Are they referring to a reference sequence? In the list they say that in the footnotes they provide more info. However, there are no footnotes.
  Have you ever had experience with tRNAdb?
  
  user14180: I have BLASTed one of the tRNA sequences. Lactobacillus acidophilus, Ile, that has insertion sites.
  
  GGGCCTATAGCTCAGCTGGTTTAGAGC_CACGCCTGATAAGCGTG_GTCGATGGTTCAAGTCCATTTAGGCCCA
  
  It looks like insertion refers to sites that exist in reference DNA but missing from tRNA sequence. But I am not a tRNA expert, it's my interpretation. See the image.
  
  
original_text: 9142: <p>I have to manually curate some tRNA sequences in order to have their original sequence without modifications. I am getting these sequences from <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/Welcome" rel="nofollow noreferrer">tRNAdb</a>. In these sequences, I found often &quot;<strong>_</strong>&quot; symbols.
  They provide this <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/images/mod.pdf" rel="nofollow noreferrer">list</a> of symbols and &quot;_&quot; corresponds to <em>insertion</em>. My question is the insertion of what? Are they referring to a reference sequence? In the <a href="http://trna.bioinf.uni-leipzig.de/DataOutput/images/mod.pdf" rel="nofollow noreferrer">list</a> they say that in the footnotes they provide more info. However, there are no footnotes.
  Have you ever had experience with tRNAdb?</p>
   14180: <p>I have BLASTed one of the tRNA sequences. Lactobacillus acidophilus, Ile, that has insertion sites.</p>
  <blockquote>
  <p>GGGCCTATAGCTCAGCTGGTTTAGAGC_CACGCCTGATAAGCGTG_GTCGATGGTTCAAGTCCATTTAGGCCCA</p>
  </blockquote>
  <p>It looks like insertion refers to sites that exist in reference DNA but missing from tRNA sequence. But I am not a tRNA expert, it's my interpretation. See the image.
  <a href="https://i.stack.imgur.com/eaCZR.png" rel="nofollow noreferrer"><img src="https://i.stack.imgur.com/eaCZR.png" alt="enter image description here" /></a></p>
  