Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    56:74 57:72 59:70 160:196 161:195 162:194 163:193 164:192
	    165:191 204:226 208:222 209:221 210:220 268:305 269:304 270:303
	    271:302 272:301
	Energy of Broken Structure: -72.3
	Energy of Pseudo-Helices:   -25.0
	Pseudoknot Energy Penalty:  31.3
	Total Free Energy:          -66.0
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-368
		Stack = -1.5  for stack of 2-367
		Stack = -2.1  for stack of 3-366
		Stack = -3.4  for stack of 4-365
		Stack = -3.3  for stack of 5-364
		Stack = -2.4  for stack of 6-363
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-362
		Stack = -3.4  for stack of 345-361
		Stack = -2.4  for stack of 346-360
		Stack = -3.3  for stack of 347-359
		Stack = -3.3  for stack of 348-358
	Helix total = -12.4
	Hairpin = 5.0  for closure of 349-357
		Stack = -2.1  for stack of 20-341
		Stack = -1.0  for stack of 21-340
		Stack = -2.1  for stack of 22-339
		Stack = -2.5  for stack of 23-338
		Stack = -1.0  for stack of 24-337
		Stack = -1.1  for stack of 25-336
		Stack = -1.3  for stack of 26-335
	Helix total = -11.1
	Internal/bulge = 1.7  for closure of 27-334	Size = 9
		Stack = -1.4  for stack of 33-329
		Stack = -2.5  for stack of 34-328
		Stack = -3.3  for stack of 35-327
		Stack = -3.3  for stack of 36-326
		Stack = -3.3  for stack of 37-325
		Stack = -2.1  for stack of 38-324
		Stack = -0.9  for stack of 39-323
		Stack = -2.2  for stack of 40-322
	Helix total = -19.0
	Internal/bulge = 3.9  for closure of 41-321	Size = 7
		Stack = -2.1  for stack of 44-315
		Stack = -2.2  for stack of 45-314
		Stack = -2.1  for stack of 46-313
		Stack = -2.4  for stack of 47-312
	Helix total = -8.8
	Multiloop = 4.7  for closure of 48-311
		Stack = -2.5  for stack of 248-287
		Stack = -2.1  for stack of 249-286
		Stack = -2.1  for stack of 250-285
		Stack = -2.5  for stack of 251-284
	Helix total = -9.2
	Internal/bulge = 1.9  for closure of 252-283	Size = 1 BP stack across bulge = -1.5
	Helix total = 0.0
	Internal/bulge = 1.0  for closure of 254-282	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 257-279	Size = 1 BP stack across bulge = -1.4
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 258-277	Size = 3
		Stack = -3.4  for stack of 261-275
		Stack = -3.3  for stack of 262-274
	Helix total = -6.7
	Hairpin = 5.3  for closure of 263-273
		Stack = -2.2  for stack of 214-245
		Stack = -3.3  for stack of 215-244
		Stack = -2.1  for stack of 216-243
		Stack = -2.1  for stack of 217-242
		Stack = -2.4  for stack of 218-241
	Helix total = -12.1
	Hairpin = 6.9  for closure of 219-240
		Stack = -2.4  for stack of 145-181
		Stack = -1.4  for stack of 146-180
		Stack = -1.5  for stack of 147-179
		Stack = -3.3  for stack of 148-178
	Helix total = -8.6
	Internal/bulge = 2.6  for closure of 149-177	Size = 6
		Stack = -2.1  for stack of 152-172
		Stack = -1.3  for stack of 153-171
		Stack = -2.1  for stack of 154-170
		Stack = -1.5  for stack of 155-169
		Stack = -2.5  for stack of 156-168
		Stack = -2.1  for stack of 157-167
	Helix total = -11.6
	Hairpin = 5.1  for closure of 158-166
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 116-142	Size = 2
		Stack = -0.9  for stack of 118-140
		Stack = -1.3  for stack of 119-139
		Stack = -0.6  for stack of 120-138
	Helix total = -2.8
	Internal/bulge = 1.9  for closure of 121-137	Size = 2
		Stack = -1.4  for stack of 123-135
		Stack = -3.4  for stack of 124-134
	Helix total = -4.8
	Hairpin = 5.0  for closure of 125-133
		Stack = -2.4  for stack of 49-64
		Stack = -2.2  for stack of 50-63
		Stack = -1.3  for stack of 51-62
		Stack = -2.1  for stack of 52-61
	Helix total = -8.0
	Hairpin = 4.9  for closure of 53-60


	Total energy = -72.3



