File: NEAR.seed

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last-align 1609-1
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# This DNA seeding scheme is good for finding short-and-strong
# (near-identical) similarities.  It is also good for similarities
# with many gaps (insertions and deletions), because it can find the
# short matches between the gaps.  (Long-and-weak seeding schemes
# allow for mismatches but not gaps.)

#lastal -r6 -q18 -a21 -b9

1  A C G T
0  ACGT

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