Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 197:238 198:237 199:236
	    200:235 201:234 202:233 203:232 252:281 253:280 254:279 255:278
	    256:277 303:342 304:341 305:340 306:339 307:338 308:337 309:336
	Energy of Broken Structure: -62.4
	Energy of Pseudo-Helices:   -42.8
	Pseudoknot Energy Penalty:  32.9
	Total Free Energy:          -72.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-403
		Stack = -1.5  for stack of 2-402
		Stack = -2.1  for stack of 3-401
		Stack = -3.4  for stack of 4-400
		Stack = -2.1  for stack of 5-399
		Stack = -2.1  for stack of 6-398
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-397
		Stack = -2.4  for stack of 380-396
		Stack = -2.1  for stack of 381-395
		Stack = -3.3  for stack of 382-394
		Stack = -3.3  for stack of 383-393
	Helix total = -11.1
	Hairpin = 4.4  for closure of 384-392
		Stack = -2.1  for stack of 19-376
		Stack = -0.6  for stack of 20-375
	Helix total = -2.7
	Internal/bulge = 3.9  for closure of 21-374	Size = 11
		Stack = -2.4  for stack of 28-368
		Stack = -0.9  for stack of 29-367
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 30-366	Size = 2
		Stack = -1.4  for stack of 32-364
		Stack = -0.5  for stack of 33-363
		Stack = -1.4  for stack of 34-362
		Stack = -1.3  for stack of 35-361
		Stack = -1.1  for stack of 36-360
		Stack = -2.1  for stack of 37-359
		Stack = -2.5  for stack of 38-358
	Helix total = -10.3
	Internal/bulge = 4.9  for closure of 39-357	Size = 9
		Stack = -2.1  for stack of 43-350
		Stack = -1.1  for stack of 44-349
		Stack = -2.1  for stack of 45-348
		Stack = -2.2  for stack of 46-347
	Helix total = -7.5
	Multiloop = 6.0  for closure of 47-346
	Helix total = 0.0
	Internal/bulge = 1.1  for closure of 283-326	Size = 6
		Stack = -2.4  for stack of 287-322
	Helix total = -2.4
	Internal/bulge = 1.2  for closure of 288-321	Size = 2
		Stack = -2.4  for stack of 290-319
	Helix total = -2.4
	Internal/bulge = -0.1  for closure of 291-318	Size = 2
		Stack = -3.4  for stack of 293-316
	Helix total = -3.4
	Internal/bulge = 3.3  for closure of 294-315	Size = 5
		Stack = -2.1  for stack of 298-312
		Stack = -3.3  for stack of 299-311
	Helix total = -5.4
	Hairpin = 5.3  for closure of 300-310
		Stack = -2.5  for stack of 241-266
		Stack = -2.1  for stack of 242-265
		Stack = -1.0  for stack of 243-264
		Stack = -2.2  for stack of 244-263
		Stack = -2.1  for stack of 245-262
		Stack = -2.1  for stack of 246-261
		Stack = -3.3  for stack of 247-260
	Helix total = -15.3
	Hairpin = 5.2  for closure of 248-259
		Stack = -2.1  for stack of 179-223
		Stack = -1.4  for stack of 180-222
		Stack = -1.5  for stack of 181-221
		Stack = -2.4  for stack of 182-220
		Stack = -3.4  for stack of 183-219
	Helix total = -10.8
	Internal/bulge = 4.4  for closure of 184-218	Size = 6
		Stack = -2.4  for stack of 186-212
		Stack = -2.4  for stack of 187-211
		Stack = -2.1  for stack of 188-210
		Stack = -3.4  for stack of 189-209
	Helix total = -10.3
	Internal/bulge = 2.2  for closure of 190-208	Size = 2
		Stack = -2.5  for stack of 192-206
		Stack = -2.1  for stack of 193-205
	Helix total = -4.6
	Hairpin = 6.2  for closure of 194-204
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 113-175	Size = 2
		Stack = -2.4  for stack of 115-173
		Stack = -2.4  for stack of 116-172
		Stack = -3.4  for stack of 117-171
		Stack = -2.1  for stack of 118-170
		Stack = -2.1  for stack of 119-169
		Stack = -3.4  for stack of 120-168
	Helix total = -15.8
	Internal/bulge = 5.0  for closure of 121-167	Size = 16
		Stack = -2.4  for stack of 127-155
		Stack = -2.4  for stack of 128-154
	Helix total = -4.8
	Internal/bulge = 1.2  for closure of 129-153	Size = 2
		Stack = -2.4  for stack of 131-151
		Stack = -0.9  for stack of 132-150
	Helix total = -3.3
	Internal/bulge = 1.4  for closure of 133-149	Size = 4
		Stack = -2.2  for stack of 136-146
	Helix total = -2.2
	Hairpin = 5.5  for closure of 137-145
		Stack = -1.5  for stack of 56-83
		Stack = -1.4  for stack of 57-82
		Stack = -2.1  for stack of 58-81
	Helix total = -5.0
	Internal/bulge = 0.5  for closure of 59-80	Size = 2
		Stack = -2.1  for stack of 61-78
	Helix total = -2.1
	Hairpin = 6.8  for closure of 62-77


	Total energy = -62.4



