Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 51:64 52:63 199:238 200:237 201:236 202:235
	    203:234 204:233 253:278 254:277 300:335 301:334 302:333 303:332
	    304:331
	Energy of Broken Structure: -65.0
	Energy of Pseudo-Helices:   -24.5
	Pseudoknot Energy Penalty:  33.2
	Total Free Energy:          -56.3
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-397
		Stack = -1.5  for stack of 2-396
		Stack = -2.1  for stack of 3-395
		Stack = -2.5  for stack of 4-394
		Stack = -0.6  for stack of 5-393
		Stack = -2.1  for stack of 6-392
	Helix total = -12.1
	Multiloop = 5.0  for closure of 7-391
		Stack = -2.4  for stack of 374-390
		Stack = -2.1  for stack of 375-389
		Stack = -3.3  for stack of 376-388
		Stack = -3.3  for stack of 377-387
	Helix total = -11.1
	Hairpin = 4.4  for closure of 378-386
		Stack = -2.4  for stack of 19-370
	Helix total = -2.4
	Internal/bulge = 2.3  for closure of 20-369	Size = 1 BP stack across bulge = -1.5
		Stack = -2.5  for stack of 21-367
		Stack = -1.4  for stack of 22-366
		Stack = -1.3  for stack of 23-365
		Stack = -2.1  for stack of 24-364
	Helix total = -7.3
	Internal/bulge = 2.8  for closure of 25-363	Size = 2
		Stack = -2.4  for stack of 28-362
		Stack = -0.9  for stack of 29-361
		Stack = -0.9  for stack of 30-360
		Stack = -1.4  for stack of 31-359
	Helix total = -5.6
	Internal/bulge = -0.7  for closure of 32-358	Size = 2
		Stack = -1.4  for stack of 34-356
		Stack = -1.3  for stack of 35-355
		Stack = -2.2  for stack of 36-354
		Stack = -2.4  for stack of 37-353
		Stack = -2.5  for stack of 38-352
	Helix total = -9.8
	Internal/bulge = 4.9  for closure of 39-351	Size = 9
		Stack = -2.1  for stack of 43-344
		Stack = -2.2  for stack of 44-343
		Stack = -2.4  for stack of 45-342
		Stack = -3.4  for stack of 46-341
	Helix total = -10.1
	Multiloop = 5.2  for closure of 47-340
	Helix total = 0.0
	Internal/bulge = 1.8  for closure of 282-321	Size = 4
		Stack = -2.1  for stack of 285-318
		Stack = -2.5  for stack of 286-317
		Stack = -0.6  for stack of 287-316
		Stack = -2.1  for stack of 288-315
		Stack = -3.4  for stack of 289-314
		Stack = -2.4  for stack of 290-313
		Stack = -3.3  for stack of 291-312
		Stack = -2.5  for stack of 292-311
	Helix total = -18.9
	Internal/bulge = 1.9  for closure of 293-310	Size = 2
		Stack = -2.1  for stack of 295-308
	Helix total = -2.1
	Hairpin = 4.9  for closure of 296-307
		Stack = 1.3  for stack of 242-267
		Stack = -1.5  for stack of 243-266
		Stack = -2.4  for stack of 244-265
		Stack = -2.5  for stack of 245-264
		Stack = -0.6  for stack of 246-263
		Stack = -1.0  for stack of 247-262
		Stack = -2.5  for stack of 248-261
		Stack = -2.1  for stack of 249-260
	Helix total = -11.3
	Hairpin = 4.3  for closure of 250-259
		Stack = -2.4  for stack of 180-223
		Stack = -2.5  for stack of 181-222
		Stack = -1.5  for stack of 182-221
		Stack = -2.4  for stack of 183-220
		Stack = -3.4  for stack of 184-219
	Helix total = -12.2
	Internal/bulge = 4.1  for closure of 185-218	Size = 4
		Stack = -2.4  for stack of 186-213
	Helix total = -2.4
	Internal/bulge = 2.0  for closure of 187-212	Size = 6
		Stack = -3.3  for stack of 191-208
		Stack = -2.4  for stack of 192-207
		Stack = -1.1  for stack of 193-206
	Helix total = -6.8
	Hairpin = 5.0  for closure of 194-205
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 114-174	Size = 2
		Stack = -1.5  for stack of 116-172
	Helix total = -1.5
	Internal/bulge = -0.1  for closure of 117-171	Size = 2
		Stack = -2.1  for stack of 119-169
		Stack = -1.0  for stack of 120-168
		Stack = -2.5  for stack of 121-167
	Helix total = -5.6
	Internal/bulge = 4.7  for closure of 122-166	Size = 15
		Stack = -2.4  for stack of 129-156
		Stack = -0.9  for stack of 130-155
	Helix total = -3.3
	Internal/bulge = 0.7  for closure of 131-154	Size = 4
	Helix total = 0.0
	Internal/bulge = 1.8  for closure of 134-151	Size = 6
		Stack = -1.0  for stack of 138-147
		Stack = -2.1  for stack of 139-146
	Helix total = -3.1
	Hairpin = 4.5  for closure of 140-145
		Stack = -2.1  for stack of 56-85
		Stack = -0.6  for stack of 57-84
		Stack = -0.9  for stack of 58-83
		Stack = -2.1  for stack of 59-82
		Stack = -1.5  for stack of 60-81
		Stack = 1.3  for stack of 61-80
	Helix total = -5.9
	Hairpin = 6.8  for closure of 62-79


	Total energy = -65.0



