Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:67 50:66 51:65 52:64 53:63 151:210 152:209 153:208
	    154:207 155:206 156:205 157:204 224:257 225:256 226:255 227:254
	    228:253 229:252 230:251 231:250 275:315 276:314 277:313 279:310
	    280:309 281:308
	Energy of Broken Structure: -99.6
	Energy of Pseudo-Helices:   -48.2
	Pseudoknot Energy Penalty:  33.4
	Total Free Energy:          -114.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-375
		Stack = -1.5  for stack of 2-374
		Stack = -2.1  for stack of 3-373
		Stack = -3.4  for stack of 4-372
		Stack = -2.1  for stack of 5-371
		Stack = -2.1  for stack of 6-370
	Helix total = -14.5
	Multiloop = 5.1  for closure of 7-369
		Stack = -3.4  for stack of 352-368
		Stack = -2.4  for stack of 353-367
		Stack = -3.3  for stack of 354-366
		Stack = -3.3  for stack of 355-365
	Helix total = -12.4
	Hairpin = 4.4  for closure of 356-364
		Stack = -2.4  for stack of 20-348
		Stack = -2.5  for stack of 21-347
		Stack = 0.3  for stack of 22-346
		Stack = -0.5  for stack of 23-345
		Stack = -2.1  for stack of 24-344
		Stack = -2.5  for stack of 25-343
		Stack = -0.5  for stack of 26-342
	Helix total = -10.2
	Internal/bulge = 4.4  for closure of 27-341	Size = 9
		Stack = -2.4  for stack of 33-336
		Stack = -2.4  for stack of 34-335
		Stack = -3.3  for stack of 35-334
	Helix total = -8.1
	Internal/bulge = 0.5  for closure of 36-333	Size = 1 BP stack across bulge = -3.3
		Stack = -2.5  for stack of 38-332
		Stack = 0.3  for stack of 39-331
		Stack = -2.1  for stack of 40-330
	Helix total = -4.3
	Internal/bulge = 3.3  for closure of 41-329	Size = 7
		Stack = -2.1  for stack of 44-323
		Stack = -1.1  for stack of 45-322
		Stack = -2.1  for stack of 46-321
		Stack = -2.2  for stack of 47-320
	Helix total = -7.5
	Multiloop = 3.6  for closure of 48-319
		Stack = -3.3  for stack of 260-295
		Stack = -2.1  for stack of 261-294
		Stack = -0.9  for stack of 262-293
		Stack = -2.4  for stack of 263-292
	Helix total = -8.7
	Internal/bulge = 0.4  for closure of 264-291	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = 2.1  for closure of 266-290	Size = 9
		Stack = -3.4  for stack of 271-284
		Stack = -2.4  for stack of 272-283
	Helix total = -5.8
	Hairpin = 4.4  for closure of 273-282
		Stack = -3.4  for stack of 213-241
		Stack = -3.3  for stack of 214-240
		Stack = -2.1  for stack of 215-239
		Stack = -1.5  for stack of 216-238
	Helix total = -10.3
	Internal/bulge = 1.2  for closure of 217-237	Size = 2
		Stack = -2.1  for stack of 219-235
		Stack = -3.4  for stack of 220-234
		Stack = -3.3  for stack of 221-233
	Helix total = -8.8
	Hairpin = 4.9  for closure of 222-232
		Stack = -3.3  for stack of 137-196
		Stack = -2.1  for stack of 138-195
		Stack = -0.9  for stack of 139-194
		Stack = -2.1  for stack of 140-193
		Stack = -3.4  for stack of 141-192
		Stack = -2.1  for stack of 142-191
	Helix total = -13.9
	Multiloop = 4.8  for closure of 143-190
		Stack = -3.4  for stack of 164-189
	Helix total = -3.4
	Internal/bulge = 0.2  for closure of 165-188	Size = 4
		Stack = -3.3  for stack of 168-185
		Stack = -1.5  for stack of 169-184
		Stack = -2.1  for stack of 170-183
		Stack = -3.3  for stack of 171-182
		Stack = -3.4  for stack of 172-181
		Stack = -3.3  for stack of 173-180
	Helix total = -16.9
	Hairpin = 3.3  for closure of 174-179
		Stack = -2.1  for stack of 145-162
		Stack = -2.1  for stack of 146-161
		Stack = -3.4  for stack of 147-160
	Helix total = -7.6
	Hairpin = 5.1  for closure of 148-159
		Stack = -2.1  for stack of 114-136
		Stack = -2.4  for stack of 115-135
		Stack = -1.4  for stack of 116-134
		Stack = -2.5  for stack of 117-133
		Stack = -3.3  for stack of 118-132
		Stack = -2.4  for stack of 119-131
	Helix total = -14.1
	Hairpin = 5.7  for closure of 120-130
		Stack = -0.9  for stack of 54-82
		Stack = -2.1  for stack of 55-81
		Stack = -2.4  for stack of 56-80
		Stack = -0.6  for stack of 57-79
		Stack = -1.4  for stack of 58-78
		Stack = -2.1  for stack of 59-77
	Helix total = -9.5
	Hairpin = 4.7  for closure of 60-76


	Total energy = -99.6



