Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:66 50:65 51:64 52:63 167:201 168:200 169:199 170:198
	    171:197 172:196 216:250 218:248 219:247 220:246 221:245 222:244
	    223:243 267:301 268:300 269:299 270:298 271:296 272:295
	Energy of Broken Structure: 1348.0
	Energy of Pseudo-Helices:   -31.5
	Pseudoknot Energy Penalty:  32.1
	Total Free Energy:          1348.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-361
		Stack = -1.5  for stack of 2-360
		Stack = -2.1  for stack of 3-359
		Stack = -3.4  for stack of 4-358
		Stack = -2.1  for stack of 5-357
		Stack = -2.1  for stack of 6-356
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-355
		Stack = -3.4  for stack of 338-354
		Stack = -2.4  for stack of 339-353
		Stack = -3.3  for stack of 340-352
		Stack = -3.3  for stack of 341-351
	Helix total = -12.4
	Hairpin = 4.4  for closure of 342-350
		Stack = -2.4  for stack of 21-334
		Stack = -2.4  for stack of 22-333
		Stack = -0.9  for stack of 23-332
		Stack = -0.9  for stack of 24-331
		Stack = -1.4  for stack of 25-330
	Helix total = -8.0
	Internal/bulge = 4.2  for closure of 26-329	Size = 15
		Stack = -2.1  for stack of 35-321
		Stack = -1.3  for stack of 36-320
	Helix total = -3.4
	Internal/bulge = 2.0  for closure of 37-319	Size = 4
		Stack = -2.4  for stack of 40-316
		Stack = -1.1  for stack of 41-315
		Stack = -1.0  for stack of 42-314
	Helix total = -4.5
	Internal/bulge = 3.7  for closure of 43-313	Size = 3
		Stack = -2.1  for stack of 44-309
		Stack = -1.1  for stack of 45-308
		Stack = -2.1  for stack of 46-307
		Stack = -2.2  for stack of 47-306
	Helix total = -7.5
	Multiloop = 3.0  for closure of 48-305
		Stack = -1.1  for stack of 252-288
		Stack = -0.9  for stack of 253-287
		Stack = -0.9  for stack of 254-286
		Stack = -0.9  for stack of 255-285
	Helix total = -3.8
	Internal/bulge = 3.7  for closure of 256-284	Size = 3
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 259-282	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.7  for closure of 261-280	Size = 4
		Stack = -2.2  for stack of 263-276
		Stack = -2.1  for stack of 264-275
	Helix total = -4.3
	Hairpin = 5.3  for closure of 265-274
		Stack = -3.4  for stack of 204-234
		Stack = -2.4  for stack of 205-233
	Helix total = -5.8
	Internal/bulge = 2.7  for closure of 206-232	Size = 7
		Stack = -2.4  for stack of 211-228
		Stack = -0.9  for stack of 212-227
		Stack = -2.2  for stack of 213-226
		Stack = -2.4  for stack of 214-225
	Helix total = -7.9
	Hairpin = 3.0  for closure of 215-224
		Stack = -2.1  for stack of 151-188
		Stack = -0.9  for stack of 152-187
		Stack = -2.4  for stack of 153-186
		Stack = -2.1  for stack of 154-185
	Helix total = -7.5
	Internal/bulge = 3.0  for closure of 155-184	Size = 5
		Stack = -2.4  for stack of 158-180
		Stack = -1.1  for stack of 159-179
		Stack = -1.3  for stack of 160-178
		Stack = -1.4  for stack of 161-177
		Stack = -1.0  for stack of 162-176
		Stack = -1.1  for stack of 163-175
		Stack = -1.3  for stack of 164-174
	Helix total = -9.6
	Hairpin = 5.5  for closure of 165-173
		Stack = -2.4  for stack of 106-150
		Stack = -2.1  for stack of 107-149
		Stack = -3.4  for stack of 108-148
		Stack = -3.3  for stack of 109-147
		Stack = -2.1  for stack of 110-146
	Helix total = -13.3
	Multiloop = 6.4  for closure of 111-145
		Stack = -2.1  for stack of 132-143
		Stack = -2.4  for stack of 133-142
	Helix total = -4.5
	Internal/bulge = 1.9  for closure of 134-141	Size = 2
	Helix total = 0.0
	Hairpin = 1400.5  for closure of 136-139
		Stack = -3.4  for stack of 112-125
		Stack = -2.1  for stack of 113-124
	Helix total = -5.5
	Internal/bulge = 1.9  for closure of 114-123	Size = 2
	Helix total = 0.0
	Hairpin = 5.1  for closure of 116-121
		Stack = -2.4  for stack of 55-75
		Stack = -2.1  for stack of 56-74
		Stack = -3.3  for stack of 57-73
		Stack = -2.2  for stack of 58-72
	Helix total = -10.0
	Hairpin = 5.1  for closure of 59-71


	Total energy = 1348.0



