There is no hard limit on the number of sequences that you can enter into the Enter Query Sequence input window or upload in a file to the BLAST® web interface. The total number of sequences that you can search with will change depending on the nature of the query sequences and the database being searched. Long sequences and large numbers of sequences in a search increase the possibility that the search will not complete due to a SIGXCPU error. If you are planning a large BLAST project you should download BLAST+ software and databases or run BLAST searches at a cloud provider.
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