text: user1456: I'm using Primer-Blast to compare a PCR template against a custom database of reference sequences, using Primer-Blast's Custom database functionality.
  However whenever I try to upload a FASTA file as the custom database and then run Primer-Blast, I get the following error:
  Exception error: Fasta Reader: sequence id ends with 80 valid nucleotide characters. Was the sequence accidentally placed in the definition line?
  No matter how I try to format my FASTA file, I get this error.
  Does anyone know how to properly format a FASTA file to have it accepted as a custom database of reference sequences to compare against the PCR template? Or is this a bug in the software?
  Here's an example FASTA file, to upload both for the template and the custom database.
  >test1
  ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAA
  AATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGG
  ACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
  CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGC
  
  
  user8629: I just copied your FASTA sequence into a file (on Mac OS) and uploaded it to Primer BLAST, the search did not give an error.
  If the error is caused by the line endings, maybe you can fix your downloaded files with a tool like dos2unix.
  Update:
  On a whim, I tried adding a description to the FASTA header:
  >test1 description
  ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAA
  AATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGG
  ACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
  CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTG
  
  This time, there was no error.
  Does that work for you as well?
  
original_text: 1456: <p>I'm using <a href="https://www.ncbi.nlm.nih.gov/tools/primer-blast/" rel="nofollow noreferrer">Primer-Blast</a> to compare a PCR template against a custom database of reference sequences, using Primer-Blast's <em>Custom</em> database functionality.</p>
  
  <p>However whenever I try to upload a FASTA file as the custom database and then run Primer-Blast, I get the following error:</p>
  
  <p><code>Exception error: Fasta Reader: sequence id ends with 80 valid nucleotide characters. Was the sequence accidentally placed in the definition line?</code></p>
  
  <p>No matter how I try to format my FASTA file, I get this error.</p>
  
  <p>Does anyone know how to properly format a FASTA file to have it accepted as a custom database of reference sequences to compare against the PCR template? Or is this a bug in the software?</p>
  
  <p>Here's an example FASTA file, to upload both for the template and the custom database.</p>
  
  <pre><code>&gt;test1
  ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAA
  AATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGG
  ACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
  CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTGC
  </code></pre>
   8629: <p>I just copied your FASTA sequence into a file (on Mac OS) and uploaded it to Primer BLAST, the search did not give an error.</p>
  
  <p>If the error is caused by the line endings, maybe you can fix your downloaded files with a tool like <a href="http://macappstore.org/dos2unix/" rel="nofollow noreferrer">dos2unix</a>.</p>
  
  <h1>Update:</h1>
  
  <p>On a whim, I tried adding a description to the FASTA header:</p>
  
  <pre><code>&gt;test1 description
  ATTAAAGGTTTATACCTTCCCAGGTAACAAACCAACCAACTTTCGATCTCTTGTAGATCTGTTCTCTAAACGAACTTTAA
  AATCTGTGTGGCTGTCACTCGGCTGCATGCTTAGTGCACTCACGCAGTATAATTAATAACTAATTACTGTCGTTGACAGG
  ACACGAGTAACTCGTCTATCTTCTGCAGGCTGCTTACGGTTTCGTCCGTGTTGCAGCCGATCATCAGCACATCTAGGTTT
  CGTCCGGGTGTGACCGAAAGGTAAGATGGAGAGCCTTGTCCCTGGTTTCAACGAGAAAACACACGTCCAACTCAGTTTG
  </code></pre>
  
  <p>This time, there was no error.</p>
  
  <p>Does that work for you as well?</p>
  