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# This matrix was derived from aligned segments of human and mouse DNA
# (F Chiaromonte, VB Yap, W Miller, PSB 2002:115-126). It is the
# default score matrix for BLASTZ v7, along with a gap existence cost
# of 400 and a gap extension cost of 30. The next line tells LAST to
# use these gap costs:
#last -a 400 -b 30
# Let's also use a minimum alignment score of 4500:
#last -e 4500
# lastex suggests that 4500 is not unreasonable for comparing
# mammalian genomes. In any case, you can override these parameters
# by setting options when running LAST. Finally, here is the matrix:
A C G T N
A 91 -114 -31 -123 -100
C -114 100 -125 -31 -100
G -31 -125 100 -114 -100
T -123 -31 -114 91 -100
N -100 -100 -100 -100 -100
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