Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 190:224 191:223 192:222
	    193:221 194:220 240:271 241:270 242:269 243:268 244:267 245:266
	    288:326 289:325 290:324 292:321 293:320 294:319
	Energy of Broken Structure: -71.0
	Energy of Pseudo-Helices:   -38.7
	Pseudoknot Energy Penalty:  32.7
	Total Free Energy:          -77.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-386
		Stack = -1.5  for stack of 2-385
		Stack = -2.1  for stack of 3-384
		Stack = -3.4  for stack of 4-383
		Stack = -3.3  for stack of 5-382
		Stack = -2.4  for stack of 6-381
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-380
		Stack = -3.3  for stack of 363-379
		Stack = -3.3  for stack of 364-378
		Stack = -3.3  for stack of 365-377
		Stack = -3.3  for stack of 366-376
	Helix total = -13.2
	Hairpin = 4.4  for closure of 367-375
		Stack = -2.4  for stack of 20-359
		Stack = -3.4  for stack of 21-358
		Stack = -3.3  for stack of 22-357
		Stack = -1.4  for stack of 23-356
		Stack = -2.1  for stack of 24-355
		Stack = -2.2  for stack of 25-354
	Helix total = -14.8
	Internal/bulge = 4.9  for closure of 26-353	Size = 14
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 35-346	Size = 7
		Stack = -3.3  for stack of 39-341
		Stack = -2.2  for stack of 40-340
		Stack = -1.0  for stack of 41-339
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 42-338	Size = 3
		Stack = -2.1  for stack of 43-334
		Stack = -1.1  for stack of 44-333
		Stack = -2.1  for stack of 45-332
		Stack = -3.4  for stack of 46-331
	Helix total = -8.7
	Multiloop = 1.4  for closure of 47-330
		Stack = -2.5  for stack of 274-308
		Stack = -3.3  for stack of 275-307
		Stack = -3.3  for stack of 276-306
	Helix total = -9.1
	Internal/bulge = 2.2  for closure of 277-305	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 281-302	Size = 7
		Stack = -3.3  for stack of 285-297
		Stack = -2.1  for stack of 286-296
	Helix total = -5.4
	Hairpin = 5.7  for closure of 287-295
		Stack = -3.4  for stack of 228-256
		Stack = -3.3  for stack of 229-255
		Stack = -2.4  for stack of 230-254
		Stack = -2.5  for stack of 231-253
	Helix total = -11.6
	Internal/bulge = 0.7  for closure of 232-252	Size = 6
		Stack = -2.2  for stack of 236-248
	Helix total = -2.2
	Hairpin = 5.9  for closure of 237-247
		Stack = -2.1  for stack of 174-210
		Stack = -0.9  for stack of 175-209
		Stack = -1.1  for stack of 176-208
		Stack = -2.4  for stack of 177-207
		Stack = -2.1  for stack of 178-206
		Stack = -1.1  for stack of 179-205
	Helix total = -9.7
	Internal/bulge = 3.3  for closure of 180-204	Size = 5
		Stack = -3.3  for stack of 183-200
		Stack = -3.3  for stack of 184-199
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 185-198	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 188-195
		Stack = -2.1  for stack of 155-173
		Stack = -2.1  for stack of 156-172
		Stack = -3.3  for stack of 157-171
	Helix total = -7.5
	Internal/bulge = 1.4  for closure of 158-170	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 160-169
		Stack = -3.3  for stack of 161-168
	Helix total = -5.5
	Hairpin = 3.7  for closure of 162-167
		Stack = -1.5  for stack of 115-154
	Helix total = -1.5
	Internal/bulge = 3.4  for closure of 116-153	Size = 6
		Stack = 0.3  for stack of 120-149
	Helix total = 0.3
	Internal/bulge = 3.4  for closure of 121-148	Size = 6
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 125-144	Size = 2
		Stack = -3.4  for stack of 127-142
		Stack = -2.1  for stack of 128-141
		Stack = -2.1  for stack of 129-140
		Stack = -3.4  for stack of 130-139
	Helix total = -11.0
	Hairpin = 3.3  for closure of 131-138
		Stack = -2.5  for stack of 55-82
		Stack = -1.0  for stack of 56-81
		Stack = -0.9  for stack of 57-80
		Stack = -2.2  for stack of 58-79
		Stack = -2.1  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -10.8
	Hairpin = 5.8  for closure of 61-76


	Total energy = -71.0



