#Nearest Neighbor parameters according to Lars Kaderali		
#pH 7.0		
#File format:		
#doubletText	dH	dS
#Doublets without values should have same as previous line		
#Watson-Crick Pairs		
AA/TT	-8400	-23.6
TT/AA		
AC/TG	-8600	-23
GT/CA		
AG/TC	-6100	-16.1
CT/GA		
AT/TA	-6500	-18.8
CA/GT	-7400	-19.3
TG/AC		
CC/GG	-6700	-15.6
GG/CC		
CG/GC	-10100	-25.5
GA/CT	-7700	-20.3
TC/AG		
GC/CG	-11100	-28.4
TA/AT	-6300	-18.5
#A-C mismatches		
AA/CT	7600	20.2
TC/AA		
AA/TC	2300	4.6
CT/AA		
AC/CG	-700	-3.8
GC/CA		
AC/TA	5300	14.6
AT/CA		
AG/CC	600	-0.6
CC/GA		
CA/AT	3400	8
TA/AC		
CA/GC	1900	3.7
CG/AC		
CC/AG	5200	14.2
GA/CC		
#C-T mismatches		
AC/TT	700	0.2
TT/CA		
AT/TC	-1200	-6.2
CT/TA		
CA/TT	1000	0.7
TT/AC		
TA/CT	1200	0.7
TC/AT		
CC/GT	-800	-4.5
TG/CC		
CC/TG	5200	13.5
GT/CC		
CG/TC	-1500	-6.1
CT/GC		
GC/CT	2300	5.4
TC/CG		
#G-A mismatches		
AA/GT	3000	7.4
TG/AA		
AA/TG	-600	-2.3
GT/AA		
AC/GG	500	3.2
GG/CA		
AG/GC	-4000	-13.2
CG/GA		
AG/TA	-700	-2.3
AT/GA		
CA/GG		
GG/AC		
GA/AT	700	0.7
TA/AG		
GA/CG	-600	-1
GC/AG		
#G-T mismatches		
AG/TT	1000	0.9
TT/GA		
AT/TG	-2500	-8.3
GT/TA		
CG/GT	-4100	-11.7
TG/GC		
CT/GG	-2800	-8
GG/TC		
GA/TT	-1300	-5.3
TT/AG		
GC/TG	-4400	-12.3
GT/CG		
GG/CT	3300	10.4
TC/GG		
TA/GT	-100	-1.7
TG/AT		
#A-A mismatches		
AA/AT	4700	12.9
TA/AA		
AA/TA	1200	1.7
AT/AA		
AC/AG	-2900	-9.8
GA/CA		
AG/AC	-900	-4.2
CA/GA		
#C-C mismatches		
AC/TC	0	-4.4
CT/CA		
CA/CT	6100	16.4
TC/AC		
CC/CG	3600	8.9
GC/CC		
CC/GC	-1500	-7.2
CG/CC		
#G-G mismatches		
AG/TG	-3100	-9.5
GT/GA		
CG/GG	-4900	-15.3
GG/GC		
GA/GT	1600	3.6
TG/AG		
GC/GG	-6000	-15.8
GG/CG		
#T-T mismatches		
AT/TT	-2700	-10.8
TT/TA		
CT/GT	-5000	-15.8
TG/TC		
GT/CT	-2200	-8.4
TC/TG		
TA/TT	200	-1.5
TT/AT		
#Dangling ends		
$A/AT	-700	-0.8
TA/A$	-700	-0.8
$A/CT	4400	14.9
TC/A$		
$A/GT	-1600	-3.6
TG/A$		
$A/TT	2900	10.4
TT/A$		
$C/AG	-2100	-3.9
GA/C$		
$C/CG	-200	-0.1
GC/C$		
$C/GG	-3900	-11.2
GG/C$		
$C/TG	-4400	-13.1
GT/C$		
$T/GA	-4100	-13.1
AG/T$		
$G/AC	-5900	-16.5
CA/G$		
$G/CC	-2600	-7.4
CC/G$		
$G/GC	-3200	-10.4
CG/G$		
$G/TC	-5200	-15
CT/G$		
A$/TG	-4200	-15
GT/$A		
$T/AA	-500	-1.1
AA/T$		
$T/CA	4700	14.2
AC/T$		
$T/TA	-3800	-12.6
AT/T$		
A$/TA	-2900	-7.6
AT/$A		
A$/TC	-4100	-13
CT/$A		
A$/TT	-200	-0.5
TT/$A		
AA/$T	200	2.3
T$/AA		
AC/$G	-6300	-17.1
G$/CA		
AG/$C	-3700	-10
C$/GA		
C$/GC	-4000	-11.9
CG/$C		
C$/GG	-3900	-10.9
GG/$C		
C$/GT	-4900	-13.8
TG/$C		
CA/$T	600	3.3
T$/AC		
CC/$G	-4400	-12.6
G$/CC		
G$/CG	-5100	-14
GC/$G		
G$/CT	-4000	-10.9
TC/$G		
GA/$T	-1100	-1.6
T$/AG		
T$/AT	-6900	-20
TA/$T		
#Double mismatches / interior loops		
INTERIOR_LOOP	0.0	-0.97
#Double gaps / bulge loops > 1		
BULGE_LOOP	0.0	-1.3
#Bulge opening and closing with match or mismatch adjacent		
BULGE_OPEN_MATCH	-2660	-14.22
BULGE_CLOSE_MATCH		
BULGE_OPEN_MISMATCH	0.0	-6.45
BULGE_CLOSE_MISMATCH		
