# base the inference on alignments in the middle half by identity
min_identity       = 25.0%    # 25th percentile
max_identity       = 75.0%    # 75th percentile

# scale scores so max substitution score will be 100, and only use
# alignments scoring at least as well as 20 ideal matches
inference_scale    = 100      # max substitution score
hsp_threshold      = 20*inference_scale
gapped_threshold   = hsp_threshold

# allow substitution score inference to iterate at most 20 times;
# don't perform gap penalty inference -- instead hardwire gap penalties
# relative to max substitution
max_sub_iterations = 20
max_gap_iterations = 0
gap_open_penalty   = 4*inference_scale
gap_extend_penalty = 0.3*inference_scale

# use all seedword positions (don't sample)
step               = 1

# adjust for entropy when qualifying HSPs
entropy            = on