Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:70 50:69 51:68 52:67 53:66 151:184 152:183 153:182
	    154:181 155:180 156:179 235:289 236:288 237:287 238:286 239:285
	    240:284 241:283 242:282 317:347 318:346 319:345
	Energy of Broken Structure: -86.9
	Energy of Pseudo-Helices:   -40.8
	Pseudoknot Energy Penalty:  38.6
	Total Free Energy:          -89.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-408
		Stack = -1.5  for stack of 2-407
		Stack = -2.1  for stack of 3-406
		Stack = -3.3  for stack of 4-405
		Stack = -3.4  for stack of 5-404
		Stack = -2.4  for stack of 6-403
	Helix total = -16.0
	Multiloop = 5.0  for closure of 7-402
		Stack = -2.4  for stack of 385-401
		Stack = -3.3  for stack of 386-400
		Stack = -3.3  for stack of 387-399
		Stack = -3.3  for stack of 388-398
	Helix total = -12.3
	Hairpin = 4.4  for closure of 389-397
		Stack = -3.3  for stack of 20-381
		Stack = -2.4  for stack of 21-380
		Stack = -1.5  for stack of 22-379
		Stack = -2.1  for stack of 23-378
	Helix total = -9.3
	Internal/bulge = 2.3  for closure of 24-377	Size = 3
		Stack = -2.5  for stack of 26-374
	Helix total = -2.5
	Internal/bulge = 2.7  for closure of 27-373	Size = 9
		Stack = -2.5  for stack of 33-368
		Stack = -1.4  for stack of 34-367
	Helix total = -3.9
	Internal/bulge = 0.9  for closure of 35-366	Size = 1 BP stack across bulge = -2.5
		Stack = -1.5  for stack of 37-365
		Stack = -2.4  for stack of 38-364
		Stack = -3.3  for stack of 39-363
		Stack = -2.5  for stack of 40-362
		Stack = 0.3  for stack of 41-361
	Helix total = -9.4
	Internal/bulge = 4.5  for closure of 42-360	Size = 5
		Stack = -2.4  for stack of 44-355
		Stack = -2.2  for stack of 45-354
		Stack = -2.1  for stack of 46-353
		Stack = -2.2  for stack of 47-352
	Helix total = -8.9
	Multiloop = 4.6  for closure of 48-351
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 304-336	Size = 2
		Stack = -2.1  for stack of 306-334
		Stack = -3.4  for stack of 307-333
		Stack = -2.4  for stack of 308-332
		Stack = -3.3  for stack of 309-331
		Stack = -3.4  for stack of 310-330
		Stack = -2.4  for stack of 311-329
	Helix total = -17.0
	Hairpin = 4.7  for closure of 312-328
		Stack = -2.5  for stack of 223-274
		Stack = -3.3  for stack of 224-273
		Stack = -2.1  for stack of 225-272
		Stack = -1.5  for stack of 226-271
		Stack = -2.4  for stack of 227-270
		Stack = -1.5  for stack of 228-269
		Stack = -2.5  for stack of 229-268
		Stack = -1.4  for stack of 230-267
	Helix total = -17.2
	Hairpin = 6.7  for closure of 231-266
		Stack = -2.4  for stack of 188-218
		Stack = -3.3  for stack of 189-217
		Stack = -3.3  for stack of 190-216
	Helix total = -9.0
	Internal/bulge = 2.7  for closure of 191-215	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 195-211	Size = 2
	Helix total = 0.0
	Hairpin = 5.5  for closure of 197-209
		Stack = -2.1  for stack of 140-166
		Stack = -1.0  for stack of 141-165
		Stack = -2.1  for stack of 142-164
		Stack = -3.4  for stack of 143-163
		Stack = -2.1  for stack of 144-162
	Helix total = -10.7
	Internal/bulge = 1.6  for closure of 145-161	Size = 1 BP stack across bulge = -2.2
		Stack = -2.1  for stack of 147-160
		Stack = -0.6  for stack of 148-159
		Stack = -2.4  for stack of 149-158
	Helix total = -5.1
	Hairpin = 3.1  for closure of 150-157
		Stack = -2.5  for stack of 116-138
		Stack = -2.4  for stack of 117-137
		Stack = -3.3  for stack of 118-136
		Stack = -3.4  for stack of 119-135
		Stack = -2.1  for stack of 120-134
		Stack = -1.3  for stack of 121-133
	Helix total = -15.0
	Hairpin = 5.9  for closure of 122-132
		Stack = -1.1  for stack of 57-82
		Stack = -2.4  for stack of 58-81
	Helix total = -3.5
	Internal/bulge = 0.5  for closure of 59-80	Size = 2
		Stack = -3.4  for stack of 61-78
		Stack = -2.1  for stack of 62-77
	Helix total = -5.5
	Hairpin = 5.2  for closure of 63-76


	Total energy = -86.9



