Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    89:155 90:154 91:153 92:152 93:151 94:150 95:148 96:147
	    97:146
	Energy of Broken Structure: -92.5
	Energy of Pseudo-Helices:   -11.7
	Pseudoknot Energy Penalty:  8.6
	Total Free Energy:          -95.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -5.0
		Stack = -2.4  for stack of 374-436
		Stack = -0.9  for stack of 375-435
		Stack = -2.2  for stack of 376-434
	Helix total = -5.5
	Internal/bulge = 1.1  for closure of 377-433	Size = 2
		Stack = -2.1  for stack of 379-431
	Helix total = -2.1
	Internal/bulge = 0.5  for closure of 380-430	Size = 1 BP stack across bulge = -3.3
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 381-428	Size = 2
		Stack = 1.3  for stack of 383-426
	Helix total = 1.3
	Internal/bulge = 7.1  for closure of 384-425	Size = 12
		Stack = -2.4  for stack of 394-421
		Stack = -2.4  for stack of 395-420
		Stack = -3.4  for stack of 396-419
		Stack = -1.4  for stack of 397-418
	Helix total = -9.6
	Internal/bulge = 3.8  for closure of 398-417	Size = 2
		Stack = -2.4  for stack of 399-414
		Stack = -3.3  for stack of 400-413
		Stack = -3.3  for stack of 401-412
	Helix total = -9.0
	Hairpin = 3.4  for closure of 402-411
		Stack = -3.3  for stack of 180-358
	Helix total = -3.3
	Internal/bulge = 0.5  for closure of 181-357	Size = 2
		Stack = -3.4  for stack of 183-355
		Stack = -2.4  for stack of 184-354
		Stack = -3.4  for stack of 185-353
	Helix total = -9.2
	Internal/bulge = 6.2  for closure of 186-352	Size = 19
		Stack = -2.4  for stack of 199-344
		Stack = -1.5  for stack of 200-343
		Stack = -2.1  for stack of 201-342
		Stack = -3.4  for stack of 202-341
		Stack = -3.3  for stack of 203-340
		Stack = -3.3  for stack of 204-339
		Stack = -2.1  for stack of 205-338
		Stack = -1.4  for stack of 206-337
		Stack = -0.5  for stack of 207-336
	Helix total = -20.0
	Internal/bulge = 1.9  for closure of 208-335	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.8  for closure of 210-333	Size = 14
		Stack = -3.3  for stack of 219-326
		Stack = -3.3  for stack of 220-325
		Stack = -2.4  for stack of 221-324
		Stack = -3.3  for stack of 222-323
		Stack = -3.4  for stack of 223-322
	Helix total = -15.7
	Internal/bulge = 2.6  for closure of 224-321	Size = 5
		Stack = -3.3  for stack of 228-318
		Stack = -2.1  for stack of 229-317
		Stack = -2.4  for stack of 230-316
		Stack = -1.4  for stack of 231-315
	Helix total = -9.2
	Multiloop = 6.9  for closure of 232-314
		Stack = -2.1  for stack of 293-305
		Stack = -2.4  for stack of 294-304
		Stack = -2.1  for stack of 295-303
	Helix total = -6.6
	Hairpin = 4.1  for closure of 296-302
		Stack = -2.4  for stack of 243-291
		Stack = -3.4  for stack of 244-290
		Stack = -2.4  for stack of 245-289
		Stack = -3.3  for stack of 246-288
	Helix total = -11.5
	Internal/bulge = 0.4  for closure of 247-287	Size = 1 BP stack across bulge = -3.4
		Stack = -2.1  for stack of 249-286
		Stack = -2.1  for stack of 250-285
		Stack = -3.4  for stack of 251-284
	Helix total = -7.6
	Internal/bulge = 2.6  for closure of 252-283	Size = 5
		Stack = -3.3  for stack of 255-279
		Stack = -1.5  for stack of 256-278
	Helix total = -4.8
	Hairpin = 4.9  for closure of 257-277
		Stack = -2.1  for stack of 4-179
		Stack = -2.4  for stack of 5-178
		Stack = -2.1  for stack of 6-177
	Helix total = -6.6
	Internal/bulge = 4.6  for closure of 7-176	Size = 4
		Stack = -0.5  for stack of 8-171
		Stack = -1.3  for stack of 9-170
	Helix total = -1.8
	Internal/bulge = 3.3  for closure of 10-169	Size = 2
		Stack = -3.3  for stack of 13-168
		Stack = -3.3  for stack of 14-167
		Stack = -1.5  for stack of 15-166
		Stack = -2.5  for stack of 16-165
		Stack = -2.4  for stack of 17-164
	Helix total = -13.0
	Internal/bulge = 1.2  for closure of 18-163	Size = 2
		Stack = -1.3  for stack of 20-161
		Stack = -0.5  for stack of 21-160
		Stack = -1.5  for stack of 22-159
	Helix total = -3.3
	Internal/bulge = 6.7  for closure of 23-158	Size = 79
		Stack = -2.5  for stack of 60-114
		Stack = -0.6  for stack of 61-113
		Stack = -2.4  for stack of 62-112
		Stack = -2.1  for stack of 63-111
	Helix total = -7.6
	Internal/bulge = 4.6  for closure of 64-110	Size = 10
		Stack = -2.4  for stack of 72-106
		Stack = -3.4  for stack of 73-105
		Stack = -2.1  for stack of 74-104
		Stack = -2.4  for stack of 75-103
		Stack = -2.4  for stack of 76-102
		Stack = -3.4  for stack of 77-101
		Stack = -2.1  for stack of 78-100
		Stack = -2.1  for stack of 79-99
	Helix total = -20.3
	Hairpin = 5.5  for closure of 80-98


	Total energy = -92.5



