// CB constraints to get the last part of the sequence in right alignment
// trying to connect herpin 125-131 137-142 to R103-108 (in parallel)

Constraint 844	1015	3 5.12 7	// CBs  R103 D125
Constraint 855	1023	3 5.12 7	// CBs	V104 I126
Constraint 862	1031	3 5.12 7	// CBs  K105 E127
Constraint 871	1040	3 5.12 7	// CBs  C106 K128
Constraint 876	1048	3 5.12 7	// CAs  V107 G129
Constraint 884	1053	3 5.12 7	// CBs  T108 T130

// hairpin constraints

Constraint 1060	1103	3 5.12 7	// CBs  K131 S137
Constraint 1053	1109	3 5.12 7	// CBs  T130 V138
Constraint 1048 1115	3 5.12 7	// CAs  G129 F139
Constraint 1040 1127	3 5.12 7	// CBs  K128 A140 

//adding HB constraints to hold the hairpin
Constraint 1047 1123	2 2.7 3.5 	// N  G129 O F139
Constraint 1049 1114	2 2.7 3.5	// O  G129 N F139
Constraint 1058	1105	2 2.7 3.5 	// N  K131 O S137
Constraint 1065	1101	2 2.7 3.5	// O  K131 N S137


// trying to get a helix to form between K113-K121
Constraint 918  982	12 13.5 15	// CAs  K113 K121

// CB constraints to change register of 2nd and 3rd strand
Constraint 362  463	3 5.12 7	// CBs  S43 L56  
Constraint 368  452	3 5.12 7	// CBs  F44 F55 
Constraint 378  447	3 5.12 7	// CAs  I45 G54   
Constraint 387  441	3 5.12 7	// CBs  T46 T53
Constraint 394  433	3 5.12 7	// CBs  S47 M52