#initialization
initH	0
initS	0
initH AT	2300
initS AT	4.1
initH GC	100
initS GC	-2.8
#matches
AA/TT	-7900	-22.2
TT/AA		
AC/TG	-8400	-22.4
GT/CA		
AG/TC	-7800	-21.0
CT/GA		
AT/TA	-7200	-20.4
CA/GT	-8500	-22.7
TG/AC		
CC/GG	-8000	-19.9
GG/CC		
CG/GC	-10600	-27.2
GA/CT	-8200	-22.2
TC/AG		
GC/CG	-9800	-24.4
TA/AT	-7200	-21.3
#Dangling ends		
AA/$T	200	2.3
AC/$G	-6300	-17.2
AG/$C	-3700	-10
AT/$A	-2900	-7.7
AA/T$	-500	-1.2
CA/G$	-5900	-16.4
GA/C$	-2100	-3.8
TA/A$	-700	-0.7
CA/$T	600	3.3
CC/$G	-4400	-12.5
CG/$C	-4000	-11.8
CT/$A	-4100	-13.2
AC/T$	4700	14.3
CC/G$	-2600	-7.4
GC/C$	-200	0.1
TC/A$	4400	14.8
GA/$T	-1100	-1.5
GC/$G	-5100	-14.1
GG/$C	-3900	-10.8
GT/$A	-4200	-15.1
AG/T$	-4100	-13.2
CG/G$	-3200	-10.3
GG/C$	-3900	-11.2
TG/A$	-1600	-3.5
TA/$T	-6900	-19.9
TC/$G	-4000	-11
TG/$C	-4900	-13.8
TT/$A	-200	-0.3
AT/T$	-3800	-12.7
CT/G$	-5200	-15.1
GT/C$	-4400	-13.1
TT/A$	2900	10.3
T$/AA	200	2.3
G$/CA	-6300	-17.2
C$/GA	-3700	-10
A$/TA	-2900	-7.7
$T/AA	-500	-1.2
$G/AC	-5900	-16.4
$C/AG	-2100	-3.8
$A/AT	-700	-0.7
T$/AC	600	3.3
G$/CC	-4400	-12.5
C$/GC	-4000	-11.8
A$/TC	-4100	-13.2
$T/CA	4700	14.3
$G/CC	-2600	-7.4
$C/CG	-200	0.1
$A/CT	4400	14.8
T$/AG	-1100	-1.5
G$/CG	-5100	-14.1
C$/GG	-3900	-10.8
A$/TG	-4200	-15.1
$T/GA	-4100	-13.2
$G/GC	-3200	-10.3
$C/GG	-3900	-11.2
$A/GT	-1600	-3.5
T$/AT	-6900	-19.9
G$/CT	-4000	-11
C$/GT	-4900	-13.8
A$/TT	-200	-0.3
$T/TA	-3800	-12.7
$G/TC	-5200	-15.1
$C/TG	-4400	-13.1
$A/TT	2900	10.3
#Terminal mismatches		
