Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 174:213 175:212 176:211
	    177:210 178:209 179:208 230:259 231:258 232:257 233:256 234:255
	    278:315 280:313 281:312 282:311 283:310 284:309
	Energy of Broken Structure: -92.8
	Energy of Pseudo-Helices:   -40.9
	Pseudoknot Energy Penalty:  32.9
	Total Free Energy:          -100.8
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-376
		Stack = -1.5  for stack of 2-375
		Stack = -2.1  for stack of 3-374
		Stack = -3.3  for stack of 4-373
		Stack = -3.4  for stack of 5-372
		Stack = -2.4  for stack of 6-371
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-370
		Stack = -3.3  for stack of 353-369
		Stack = -3.3  for stack of 354-368
		Stack = -3.3  for stack of 355-367
		Stack = -3.3  for stack of 356-366
	Helix total = -13.2
	Hairpin = 4.4  for closure of 357-365
		Stack = -2.4  for stack of 20-349
		Stack = -3.4  for stack of 21-348
		Stack = -3.3  for stack of 22-347
		Stack = -2.4  for stack of 23-346
		Stack = -3.3  for stack of 24-345
		Stack = -2.5  for stack of 25-344
		Stack = 0.3  for stack of 26-343
	Helix total = -17.0
	Internal/bulge = 2.3  for closure of 27-342	Size = 9
		Stack = -3.3  for stack of 33-337
		Stack = -3.3  for stack of 34-336
	Helix total = -6.6
	Internal/bulge = 0.4  for closure of 35-335	Size = 6
		Stack = -3.3  for stack of 39-331
		Stack = -2.5  for stack of 40-330
	Helix total = -5.8
	Internal/bulge = 4.5  for closure of 41-329	Size = 5
		Stack = -2.1  for stack of 43-324
		Stack = -1.1  for stack of 44-323
		Stack = -2.1  for stack of 45-322
		Stack = -3.4  for stack of 46-321
	Helix total = -8.7
	Multiloop = 4.2  for closure of 47-320
		Stack = -2.5  for stack of 263-298
		Stack = -2.4  for stack of 264-297
		Stack = -2.2  for stack of 265-296
		Stack = -2.4  for stack of 266-295
	Helix total = -9.5
	Internal/bulge = 0.5  for closure of 267-294	Size = 1 BP stack across bulge = -3.3
		Stack = -2.1  for stack of 269-293
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 270-292	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 272-290	Size = 3
		Stack = -2.4  for stack of 274-287
		Stack = -3.3  for stack of 275-286
	Helix total = -5.7
	Hairpin = 4.1  for closure of 276-285
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 215-247	Size = 2
		Stack = -3.4  for stack of 217-245
		Stack = -2.4  for stack of 218-244
		Stack = -3.3  for stack of 219-243
		Stack = -2.5  for stack of 220-242
		Stack = -0.6  for stack of 221-241
		Stack = -2.1  for stack of 222-240
		Stack = -1.5  for stack of 223-239
		Stack = -2.5  for stack of 224-238
	Helix total = -18.3
	Internal/bulge = 0.6  for closure of 225-237	Size = 2
	Helix total = 0.0
	Hairpin = 4.6  for closure of 227-235
		Stack = -2.1  for stack of 147-199
		Stack = -1.3  for stack of 148-198
	Helix total = -3.4
	Internal/bulge = 1.9  for closure of 149-197	Size = 2
		Stack = -1.3  for stack of 151-195
	Helix total = -1.3
	Internal/bulge = 5.8  for closure of 152-194	Size = 7
		Stack = -3.3  for stack of 159-192
		Stack = -3.3  for stack of 160-191
		Stack = -1.4  for stack of 161-190
	Helix total = -8.0
	Internal/bulge = 1.7  for closure of 162-189	Size = 6
		Stack = -2.2  for stack of 166-185
		Stack = -2.1  for stack of 167-184
		Stack = -2.4  for stack of 168-183
		Stack = -1.1  for stack of 169-182
		Stack = -2.1  for stack of 170-181
	Helix total = -9.9
	Hairpin = 3.9  for closure of 171-180
		Stack = -2.1  for stack of 125-146
		Stack = -1.0  for stack of 126-145
		Stack = -2.1  for stack of 127-144
		Stack = -3.4  for stack of 128-143
		Stack = -2.1  for stack of 129-142
		Stack = -2.1  for stack of 130-141
	Helix total = -12.8
	Hairpin = 4.4  for closure of 131-140
		Stack = -2.4  for stack of 54-83
		Stack = -2.2  for stack of 55-82
		Stack = -1.3  for stack of 56-81
		Stack = -0.9  for stack of 57-80
		Stack = -2.2  for stack of 58-79
		Stack = -2.4  for stack of 59-78
	Helix total = -11.4
	Hairpin = 5.9  for closure of 60-77


	Total energy = -92.8



