Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    57:83 58:82 59:81 62:78 63:77 153:194 154:193 155:192
	    156:191 157:190 158:189 210:237 211:236 212:235 213:234 255:294
	    257:292 259:288 260:287 261:286
	Energy of Broken Structure: 1355.0
	Energy of Pseudo-Helices:   -27.3
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          1359.2
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 = -2.4  for stack of 4-352
		Stack = -1.1  for stack of 5-351
		Stack = -2.1  for stack of 6-350
	Helix total = -12.5
	Multiloop = 5.2  for closure of 7-349
		Stack = -3.4  for stack of 332-348
		Stack = -2.4  for stack of 333-347
		Stack = -3.3  for stack of 334-346
		Stack = -3.3  for stack of 335-345
	Helix total = -12.4
	Hairpin = 4.4  for closure of 336-344
		Stack = -2.4  for stack of 21-328
		Stack = -3.4  for stack of 22-327
		Stack = -3.3  for stack of 23-326
		Stack = -1.4  for stack of 24-325
		Stack = -1.3  for stack of 25-324
		Stack = -1.4  for stack of 26-323
		Stack = 0.3  for stack of 27-322
	Helix total = -12.9
	Internal/bulge = 1.9  for closure of 28-321	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.9  for closure of 30-319	Size = 5
		Stack = -2.5  for stack of 34-316
		Stack = -2.1  for stack of 35-315
		Stack = -2.4  for stack of 36-314
	Helix total = -7.0
	Internal/bulge = 2.7  for closure of 37-313	Size = 6
		Stack = -1.3  for stack of 41-309
		Stack = -1.1  for stack of 42-308
		Stack = -1.0  for stack of 43-307
	Helix total = -3.4
	Internal/bulge = 3.7  for closure of 44-306	Size = 3
		Stack = -2.1  for stack of 45-302
		Stack = -1.1  for stack of 46-301
		Stack = -2.1  for stack of 47-300
		Stack = -3.4  for stack of 48-299
	Helix total = -8.7
	Multiloop = 6.2  for closure of 49-298
		Stack = -2.5  for stack of 241-275
		Stack = -1.4  for stack of 242-274
		Stack = -1.4  for stack of 243-273
		Stack = -0.9  for stack of 244-272
	Helix total = -6.2
	Internal/bulge = 3.0  for closure of 245-271	Size = 3
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 248-269	Size = 7
		Stack = -3.3  for stack of 252-264
		Stack = -2.1  for stack of 253-263
	Helix total = -5.4
	Hairpin = 5.7  for closure of 254-262
		Stack = -1.4  for stack of 197-223
		Stack = -1.3  for stack of 198-222
	Helix total = -2.7
	Internal/bulge = 3.7  for closure of 199-221	Size = 4
		Stack = -2.1  for stack of 203-219
		Stack = -2.5  for stack of 204-218
		Stack = -1.5  for stack of 205-217
	Helix total = -6.1
	Hairpin = 5.0  for closure of 206-216
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 139-179	Size = 2
		Stack = -2.5  for stack of 141-177
	Helix total = -2.5
	Internal/bulge = 2.2  for closure of 142-176	Size = 3
	Helix total = 0.0
	Internal/bulge = 6.2  for closure of 144-173	Size = 10
		Stack = -2.1  for stack of 147-164
		Stack = -2.1  for stack of 148-163
		Stack = -2.4  for stack of 149-162
	Helix total = -6.6
	Internal/bulge = 1.9  for closure of 150-161	Size = 2
	Helix total = 0.0
	Hairpin = 5.1  for closure of 152-159
		Stack = -2.1  for stack of 118-135
		Stack = -3.4  for stack of 119-134
		Stack = -2.1  for stack of 120-133
		Stack = -2.1  for stack of 121-132
		Stack = -3.4  for stack of 122-131
		Stack = -3.3  for stack of 123-130
		Stack = -2.1  for stack of 124-129
	Helix total = -18.5
	Hairpin = 1400.5  for closure of 125-128
		Stack = -2.4  for stack of 50-69
		Stack = -2.4  for stack of 51-68
		Stack = -2.1  for stack of 52-67
		Stack = -2.4  for stack of 53-66
	Helix total = -9.3
	Hairpin = 6.0  for closure of 54-65


	Total energy = 1355.0



