Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 160:195 161:194 162:193
	    163:192 164:191 165:190 210:245 212:243 213:242 214:241 215:240
	    216:239 217:238 263:305 264:304 265:303 266:302 267:301 268:300
	    269:299 271:297
	Energy of Broken Structure: -89.3
	Energy of Pseudo-Helices:   -44.6
	Pseudoknot Energy Penalty:  36.0
	Total Free Energy:          -97.9
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-365
		Stack = -1.5  for stack of 2-364
		Stack = -2.1  for stack of 3-363
		Stack = -2.4  for stack of 4-362
		Stack = -1.1  for stack of 5-361
		Stack = -2.1  for stack of 6-360
	Helix total = -12.5
	Multiloop = 5.0  for closure of 7-359
		Stack = -3.3  for stack of 342-358
		Stack = -3.3  for stack of 343-357
		Stack = -3.3  for stack of 344-356
		Stack = -3.3  for stack of 345-355
	Helix total = -13.2
	Hairpin = 4.4  for closure of 346-354
		Stack = -2.4  for stack of 19-338
		Stack = -3.4  for stack of 20-337
	Helix total = -5.8
	Internal/bulge = 0.5  for closure of 21-336	Size = 2
		Stack = -2.5  for stack of 23-334
	Helix total = -2.5
	Internal/bulge = 1.6  for closure of 24-333	Size = 2
		Stack = -2.1  for stack of 26-331
	Helix total = -2.1
	Internal/bulge = 2.7  for closure of 27-330	Size = 7
		Stack = -2.1  for stack of 32-326
		Stack = -1.5  for stack of 33-325
		Stack = -2.4  for stack of 34-324
		Stack = -2.2  for stack of 35-323
		Stack = -2.1  for stack of 36-322
		Stack = -1.5  for stack of 37-321
	Helix total = -11.8
	Internal/bulge = 3.4  for closure of 38-320	Size = 10
		Stack = -2.4  for stack of 43-313
		Stack = -3.3  for stack of 44-312
		Stack = -3.3  for stack of 45-311
		Stack = -2.2  for stack of 46-310
	Helix total = -11.2
	Multiloop = 6.5  for closure of 47-309
		Stack = -2.1  for stack of 246-284
		Stack = -3.4  for stack of 247-283
		Stack = -3.3  for stack of 248-282
		Stack = -2.1  for stack of 249-281
	Helix total = -10.9
	Internal/bulge = 3.8  for closure of 250-280	Size = 2
		Stack = -2.1  for stack of 253-279
		Stack = -2.4  for stack of 254-278
		Stack = -1.1  for stack of 255-277
		Stack = -0.9  for stack of 256-276
		Stack = -1.3  for stack of 257-275
	Helix total = -7.8
	Hairpin = 6.4  for closure of 258-274
		Stack = -3.3  for stack of 199-228
		Stack = -2.4  for stack of 200-227
	Helix total = -5.7
	Internal/bulge = 0.5  for closure of 201-226	Size = 1 BP stack across bulge = -3.3
		Stack = -2.2  for stack of 203-225
		Stack = -2.1  for stack of 204-224
		Stack = -2.2  for stack of 205-223
		Stack = -0.9  for stack of 206-222
		Stack = -1.3  for stack of 207-221
		Stack = 0.3  for stack of 208-220
	Helix total = -8.4
	Hairpin = 6.3  for closure of 209-219
		Stack = -2.1  for stack of 144-181
		Stack = -2.5  for stack of 145-180
		Stack = -1.5  for stack of 146-179
		Stack = -2.4  for stack of 147-178
		Stack = -3.3  for stack of 148-177
	Helix total = -11.8
	Internal/bulge = 2.2  for closure of 149-176	Size = 3
		Stack = -1.4  for stack of 151-173
		Stack = -1.0  for stack of 152-172
		Stack = -2.1  for stack of 153-171
		Stack = -3.3  for stack of 154-170
		Stack = -3.3  for stack of 155-169
		Stack = -3.4  for stack of 156-168
	Helix total = -14.5
	Hairpin = 5.4  for closure of 157-167
		Stack = -2.4  for stack of 112-143
		Stack = -1.1  for stack of 113-142
		Stack = -2.4  for stack of 114-141
		Stack = -2.1  for stack of 115-140
		Stack = -1.3  for stack of 116-139
		Stack = -0.9  for stack of 117-138
		Stack = -2.1  for stack of 118-137
	Helix total = -12.3
	Internal/bulge = 3.7  for closure of 119-136	Size = 3
		Stack = -1.4  for stack of 123-135
		Stack = -3.4  for stack of 124-134
		Stack = -2.1  for stack of 125-133
	Helix total = -6.9
	Hairpin = 4.2  for closure of 126-132
		Stack = -2.1  for stack of 54-83
		Stack = -3.4  for stack of 55-82
		Stack = -2.4  for stack of 56-81
		Stack = -2.4  for stack of 57-80
		Stack = -2.1  for stack of 58-79
	Helix total = -12.4
	Hairpin = 5.6  for closure of 59-78


	Total energy = -89.3



