Why does the program crash when I try to load an alignment processed by ClustalW on the web as a .aln file?
The crash is due to the length of the sequence name. Primer Premier uses publicly available ClustalW code to perform the alignment. Unfortunately, the available version supports sequence names of 15 characters or less. Please truncate the sequence name to 15 characters (max.) before aligning the sequences with ClustalW. Loading the output .aln file will not crash the program.
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