# Limits
left_flank_length = 0
right_flank_length = 0
# Base Cost
rrf_cost = 4
rqf_cost = 4
qrf_cost = 4
qqf_cost = 4
rrr_cost = 3
rqr_cost = 2
qrr_cost = 2
qqr_cost = 3
# Jump Costs
RQQROffset
-inf -100 101
inf 0 inf
RRQQOffset
-inf -100 1
inf 0 inf
Length
0 3
inf 0
LengthDifference
-inf -100 101
inf 0 inf
ForwardAntiPrimaryGap
-inf -100 101
0 0 inf
ReverseAntiPrimaryGap
-inf -100 101
inf 0 inf
# 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 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
# 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