Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:83 57:82 58:81 59:80 199:233 200:232 201:231 202:230
	    203:229 204:228 238:264 240:262 241:261 245:257 246:256 300:338
	    301:337 302:336 303:335 304:334 305:333
	Energy of Broken Structure: 1338.0
	Energy of Pseudo-Helices:   -35.9
	Pseudoknot Energy Penalty:  31.7
	Total Free Energy:          1333.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-398
		Stack = -3.3  for stack of 2-397
		Stack = -3.3  for stack of 3-396
		Stack = -2.4  for stack of 4-395
	Helix total = -12.3
	Multiloop = 5.6  for closure of 5-394
	Helix total = 0.0
	Internal/bulge = 0.2  for closure of 375-391	Size = 4
	Helix total = 0.0
	Hairpin = 3.9  for closure of 378-388
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 17-373	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 19-371	Size = 1 BP stack across bulge = -2.4
		Stack = -3.4  for stack of 21-370
		Stack = -2.4  for stack of 22-369
	Helix total = -5.8
	Internal/bulge = 1.0  for closure of 23-368	Size = 16
	Helix total = 0.0
	Internal/bulge = -2.3  for closure of 32-359	Size = 2
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 34-357	Size = 2
	Helix total = 0.0
	Internal/bulge = -2.2  for closure of 36-355	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.8  for closure of 38-353	Size = 14
		Stack = -1.4  for stack of 45-344
	Helix total = -1.4
	Multiloop = 3.1  for closure of 46-343
		Stack = -3.3  for stack of 284-320
		Stack = -3.4  for stack of 285-319
		Stack = -3.3  for stack of 286-318
		Stack = -3.3  for stack of 287-317
	Helix total = -13.3
	Internal/bulge = 2.8  for closure of 288-316	Size = 2
		Stack = -2.4  for stack of 291-315
		Stack = -3.3  for stack of 292-314
		Stack = -3.4  for stack of 293-313
		Stack = -2.4  for stack of 294-312
		Stack = -2.4  for stack of 295-311
	Helix total = -13.9
	Hairpin = 6.7  for closure of 296-310
		Stack = -1.4  for stack of 247-283
		Stack = -2.1  for stack of 248-282
		Stack = -2.2  for stack of 249-281
		Stack = -2.4  for stack of 250-280
		Stack = -2.1  for stack of 251-279
		Stack = -2.2  for stack of 252-278
	Helix total = -12.4
	Hairpin = 5.1  for closure of 253-277
		Stack = -2.1  for stack of 184-220
		Stack = -2.5  for stack of 185-219
		Stack = -1.5  for stack of 186-218
		Stack = -2.1  for stack of 187-217
		Stack = -2.1  for stack of 188-216
	Helix total = -10.3
	Internal/bulge = 2.3  for closure of 189-215	Size = 4
		Stack = -3.3  for stack of 191-211
		Stack = -2.4  for stack of 192-210
		Stack = -3.3  for stack of 193-209
		Stack = -3.3  for stack of 194-208
	Helix total = -12.3
	Hairpin = 4.1  for closure of 195-207
		Stack = -1.5  for stack of 114-181
		Stack = -2.1  for stack of 115-180
	Helix total = -3.6
	Internal/bulge = 1.6  for closure of 116-179	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.5  for closure of 119-176	Size = 10
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 125-170	Size = 12
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 132-163	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 134-161	Size = 2
		Stack = -2.4  for stack of 136-159
		Stack = -2.4  for stack of 137-158
		Stack = -3.4  for stack of 138-157
	Helix total = -8.2
	Internal/bulge = 1.2  for closure of 139-156	Size = 2
		Stack = -2.5  for stack of 141-154
		Stack = -3.3  for stack of 142-153
		Stack = -2.1  for stack of 143-152
		Stack = -2.1  for stack of 144-151
		Stack = -2.4  for stack of 145-150
	Helix total = -12.4
	Hairpin = 1400.5  for closure of 146-149
		Stack = -2.4  for stack of 48-69
		Stack = -2.4  for stack of 49-68
		Stack = -2.1  for stack of 50-67
		Stack = -1.5  for stack of 51-66
	Helix total = -8.4
	Hairpin = 6.9  for closure of 52-65


	Total energy = 1338.0



