Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    51:72 52:71 54:69 55:68 157:190 158:189 159:188 160:187
	    161:186 162:185 206:237 207:236 208:235 209:234 210:233 211:232
	    212:231 240:275 244:271 248:268 249:267 252:262
	Energy of Broken Structure: -66.7
	Energy of Pseudo-Helices:   -28.5
	Pseudoknot Energy Penalty:  32.9
	Total Free Energy:          -62.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-355
		Stack = -1.5  for stack of 2-354
		Stack = -2.1  for stack of 3-353
		Stack = -3.3  for stack of 4-352
		Stack = -3.4  for stack of 5-351
		Stack = -2.4  for stack of 6-350
	Helix total = -16.0
	Multiloop = 6.6  for closure of 7-349
		Stack = -2.1  for stack of 332-348
		Stack = -3.3  for stack of 333-347
		Stack = -3.3  for stack of 334-346
		Stack = -3.3  for stack of 335-345
	Helix total = -12.0
	Hairpin = 4.4  for closure of 336-344
		Stack = -2.4  for stack of 21-328
		Stack = -1.5  for stack of 22-327
		Stack = -0.5  for stack of 23-326
		Stack = -0.5  for stack of 24-325
		Stack = -1.3  for stack of 25-324
		Stack = -1.1  for stack of 26-323
		Stack = -2.1  for stack of 27-322
	Helix total = -9.4
	Internal/bulge = 1.2  for closure of 28-321	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 30-319	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 33-318	Size = 2
		Stack = -1.4  for stack of 35-316
		Stack = -1.4  for stack of 36-315
		Stack = -0.9  for stack of 37-314
		Stack = -0.9  for stack of 38-313
		Stack = -1.0  for stack of 39-312
		Stack = -1.3  for stack of 40-311
		Stack = -2.1  for stack of 41-310
	Helix total = -9.0
	Internal/bulge = 1.2  for closure of 42-309	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.5  for closure of 44-307	Size = 5
		Stack = -2.4  for stack of 46-302
		Stack = -2.4  for stack of 47-301
		Stack = -2.1  for stack of 48-300
		Stack = -2.2  for stack of 49-299
	Helix total = -9.1
	Multiloop = 5.0  for closure of 50-298
		Stack = -2.2  for stack of 255-294
		Stack = -0.9  for stack of 256-293
		Stack = -0.9  for stack of 257-292
		Stack = -2.1  for stack of 258-291
		Stack = -2.2  for stack of 259-290
		Stack = -1.3  for stack of 260-289
	Helix total = -9.6
	Hairpin = 6.3  for closure of 261-288
		Stack = -3.3  for stack of 193-224
		Stack = -2.4  for stack of 194-223
	Helix total = -5.7
	Internal/bulge = 0.1  for closure of 195-222	Size = 4
		Stack = -3.3  for stack of 198-219
		Stack = -2.1  for stack of 199-218
		Stack = -0.9  for stack of 200-217
		Stack = -1.3  for stack of 201-216
		Stack = -2.2  for stack of 202-215
	Helix total = -9.8
	Hairpin = 5.0  for closure of 203-214
		Stack = -2.4  for stack of 143-178
		Stack = -2.5  for stack of 144-177
		Stack = -1.5  for stack of 145-176
		Stack = -2.1  for stack of 146-175
		Stack = -2.1  for stack of 147-174
	Helix total = -10.6
	Internal/bulge = 2.3  for closure of 148-173	Size = 4
		Stack = -2.1  for stack of 150-169
		Stack = -2.1  for stack of 151-168
		Stack = -2.4  for stack of 152-167
		Stack = -2.1  for stack of 153-166
	Helix total = -8.7
	Hairpin = 5.4  for closure of 154-165
		Stack = -0.9  for stack of 123-142
		Stack = -1.3  for stack of 124-141
		Stack = -2.1  for stack of 125-140
		Stack = -3.4  for stack of 126-139
		Stack = -2.1  for stack of 127-138
		Stack = -2.1  for stack of 128-137
	Helix total = -11.9
	Hairpin = 4.9  for closure of 129-136
		Stack = -3.3  for stack of 59-87
		Stack = -2.1  for stack of 60-86
		Stack = -1.0  for stack of 61-85
		Stack = -1.4  for stack of 62-84
		Stack = -1.0  for stack of 63-83
		Stack = -2.1  for stack of 64-82
	Helix total = -10.9
	Hairpin = 5.8  for closure of 65-81


	Total energy = -66.7



