# Limits
left_flank_length = 0
right_flank_length = 0
# Base Cost
rrf_cost = inf
rqf_cost = inf
qrf_cost = inf
qqf_cost = inf
rrr_cost = 2
rqr_cost = 2
qrr_cost = 2
qqr_cost = 2
# Jump Costs
RQQROffset
-inf -300 301
inf 0 inf
RRQQOffset
-inf -300 1
inf 0 inf
Length
0 5 6 7 8 1000
inf 15 10 5 0 inf
LengthDifference
-inf -500 501
inf 0 inf
ForwardAntiPrimaryGap
-inf 1
0 inf
ReverseAntiPrimaryGap
-inf
0
# Primary Edit Costs
SubstitutionCostTable
| A C G T N
--+---------------
A | 0 2 2 2 1
C | 2 0 2 2 1
G | 2 2 0 2 1
T | 2 2 2 0 1
N | 1 1 1 1 1
GapOpenCostVector
A C G T N
3 3 3 3 3
GapExtendCostVector
A C G T N
1 1 1 1 1
# Secondary Forward Edit Costs
SubstitutionCostTable
| A C G T N
--+---------------
A | 0 2 2 2 1
C | 2 0 2 2 1
G | 2 2 0 2 1
T | 2 2 2 0 1
N | 1 1 1 1 1
GapOpenCostVector
A C G T N
3 3 3 3 3
GapExtendCostVector
A C G T N
1 1 1 1 1
# Secondary Reverse Edit Costs
SubstitutionCostTable
| A C G T N
--+---------------
A | 0 4 4 4 2
C | 4 0 4 4 2
G | 4 4 0 4 2
T | 4 4 4 0 2
N | 2 2 2 2 2
GapOpenCostVector
A C G T N
6 6 6 6 6
GapExtendCostVector
A C G T N
2 2 2 2 2
# Left Flank Edit Costs
SubstitutionCostTable
| A C G T N
--+---------------
A | 0 2 2 2 0
C | 2 0 2 2 0
G | 2 2 0 2 0
T | 2 2 2 0 0
N | 0 0 0 0 0
GapOpenCostVector
A C G T N
3 3 3 3 3
GapExtendCostVector
A C G T N
1 1 1 1 1
# Right Flank Edit Costs
SubstitutionCostTable
| A C G T N
--+---------------
A | 0 2 2 2 0
C | 2 0 2 2 0
G | 2 2 0 2 0
T | 2 2 2 0 0
N | 0 0 0 0 0
GapOpenCostVector
A C G T N
3 3 3 3 3
GapExtendCostVector
A C G T N
1 1 1 1 1