Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    55:79 56:78 57:77 58:76 150:206 151:205 152:204 153:203
	    154:202 155:201 222:258 223:257 224:256 225:255 226:254 227:253
	    228:252 229:251 230:250 274:314 275:313 276:312 277:311 278:310
	    279:309 280:308
	Energy of Broken Structure: -98.0
	Energy of Pseudo-Helices:   -48.0
	Pseudoknot Energy Penalty:  32.4
	Total Free Energy:          -113.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-374
		Stack = -1.5  for stack of 2-373
		Stack = -2.1  for stack of 3-372
		Stack = -3.4  for stack of 4-371
		Stack = -3.3  for stack of 5-370
		Stack = -2.4  for stack of 6-369
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-368
		Stack = -3.3  for stack of 351-367
		Stack = -3.3  for stack of 352-366
		Stack = -3.3  for stack of 353-365
		Stack = -3.3  for stack of 354-364
	Helix total = -13.2
	Hairpin = 4.4  for closure of 355-363
		Stack = -2.4  for stack of 20-347
		Stack = -2.5  for stack of 21-346
		Stack = 0.3  for stack of 22-345
		Stack = -0.5  for stack of 23-344
		Stack = -2.1  for stack of 24-343
		Stack = -2.5  for stack of 25-342
		Stack = -1.5  for stack of 26-341
	Helix total = -11.2
	Internal/bulge = 2.7  for closure of 27-340	Size = 9
		Stack = -2.5  for stack of 33-335
		Stack = -2.1  for stack of 34-334
		Stack = -2.1  for stack of 35-333
	Helix total = -6.7
	Internal/bulge = 1.5  for closure of 36-332	Size = 3
		Stack = -2.1  for stack of 39-330
		Stack = -2.1  for stack of 40-329
		Stack = -2.5  for stack of 41-328
	Helix total = -6.7
	Internal/bulge = 4.5  for closure of 42-327	Size = 5
		Stack = -2.1  for stack of 44-322
		Stack = -1.1  for stack of 45-321
		Stack = -1.3  for stack of 46-320
		Stack = -2.2  for stack of 47-319
	Helix total = -6.7
	Multiloop = 0.8  for closure of 48-318
		Stack = -3.4  for stack of 259-295
		Stack = -2.1  for stack of 260-294
	Helix total = -5.5
	Internal/bulge = 2.9  for closure of 261-293	Size = 11
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 268-287	Size = 2
		Stack = -2.1  for stack of 269-284
		Stack = -3.4  for stack of 270-283
		Stack = -3.3  for stack of 271-282
	Helix total = -8.8
	Hairpin = 4.1  for closure of 272-281
		Stack = -3.4  for stack of 210-241
	Helix total = -3.4
	Internal/bulge = 1.2  for closure of 211-240	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 213-238	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 215-237
		Stack = -2.1  for stack of 216-236
		Stack = -1.5  for stack of 217-235
		Stack = -2.1  for stack of 218-234
		Stack = -3.4  for stack of 219-233
	Helix total = -11.2
	Hairpin = 5.6  for closure of 220-232
		Stack = -1.4  for stack of 135-193
		Stack = -2.5  for stack of 136-192
		Stack = -2.1  for stack of 137-191
		Stack = -2.1  for stack of 138-190
		Stack = -3.4  for stack of 139-189
		Stack = -2.1  for stack of 140-188
	Helix total = -13.6
	Multiloop = 7.8  for closure of 141-187
		Stack = -2.5  for stack of 162-186
		Stack = -1.4  for stack of 163-185
		Stack = -3.3  for stack of 164-184
		Stack = -2.5  for stack of 165-183
	Helix total = -9.7
	Internal/bulge = 1.9  for closure of 166-182	Size = 1 BP stack across bulge = -1.5
		Stack = -3.3  for stack of 168-181
		Stack = -2.1  for stack of 169-180
		Stack = -2.1  for stack of 170-179
		Stack = -3.4  for stack of 171-178
	Helix total = -10.9
	Hairpin = 3.3  for closure of 172-177
		Stack = -3.3  for stack of 142-161
		Stack = -2.4  for stack of 143-160
		Stack = -3.3  for stack of 144-159
		Stack = -3.4  for stack of 145-158
	Helix total = -12.4
	Hairpin = 5.1  for closure of 146-157
		Stack = -2.1  for stack of 113-134
		Stack = -1.5  for stack of 114-133
		Stack = -2.4  for stack of 115-132
		Stack = -3.4  for stack of 116-131
		Stack = -3.3  for stack of 117-130
		Stack = -2.4  for stack of 118-129
	Helix total = -15.1
	Hairpin = 4.8  for closure of 119-128
		Stack = -2.4  for stack of 49-66
		Stack = -2.4  for stack of 50-65
		Stack = -2.1  for stack of 51-64
		Stack = -3.3  for stack of 52-63
	Helix total = -10.2
	Hairpin = 4.4  for closure of 53-62


	Total energy = -98.0



