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memory requirements for alignment

See also
Reducing memory
32-bit and 64-bit binaries

  Memory requirements for a database index

The amount of memory required to align a pair of sequences scales like the product of the sequence lengths. In the worst case, approximately 4NM bytes may be needed, where N and M are the sequence lengths. For very long sequences, say 20k or more, this can be a lot: 4 x 20k x 20k = 1.6 Gb.

If multi-threading is used, then each thread may be doing its own alignment, so the worst-case memory requirement scales like 4NMt where t is the number of threads.