Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    49:72 50:71 51:70 52:69 53:68 175:238 176:237 177:236
	    178:235 179:234 180:233 181:232 253:282 254:281 255:280 256:279
	    257:278 301:338 302:337 303:336 304:335 306:333 307:332 308:331
	Energy of Broken Structure: -108.5
	Energy of Pseudo-Helices:   -45.5
	Pseudoknot Energy Penalty:  40.8
	Total Free Energy:          -113.2
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-400
		Stack = -1.5  for stack of 2-399
		Stack = -2.1  for stack of 3-398
		Stack = -2.4  for stack of 4-397
		Stack = -1.1  for stack of 5-396
		Stack = -2.1  for stack of 6-395
	Helix total = -12.5
	Multiloop = 5.1  for closure of 7-394
		Stack = -3.4  for stack of 377-393
		Stack = -2.4  for stack of 378-392
		Stack = -3.3  for stack of 379-391
		Stack = -3.3  for stack of 380-390
	Helix total = -12.4
	Hairpin = 4.4  for closure of 381-389
		Stack = -2.1  for stack of 20-373
		Stack = -2.1  for stack of 21-372
		Stack = -3.3  for stack of 22-371
		Stack = -2.4  for stack of 23-370
		Stack = -1.4  for stack of 24-369
		Stack = -1.0  for stack of 25-368
	Helix total = -12.3
	Internal/bulge = 2.6  for closure of 26-367	Size = 3
		Stack = -2.1  for stack of 29-365
		Stack = -2.5  for stack of 30-364
	Helix total = -4.6
	Internal/bulge = -0.3  for closure of 31-363	Size = 4
		Stack = -2.4  for stack of 34-360
		Stack = -1.1  for stack of 35-359
		Stack = -2.1  for stack of 36-358
		Stack = -2.5  for stack of 37-357
	Helix total = -8.1
	Internal/bulge = 1.2  for closure of 38-356	Size = 2
		Stack = -2.2  for stack of 40-354
		Stack = -0.9  for stack of 41-353
		Stack = -1.0  for stack of 42-352
	Helix total = -4.1
	Internal/bulge = 3.7  for closure of 43-351	Size = 3
		Stack = -2.1  for stack of 44-347
		Stack = -2.2  for stack of 45-346
		Stack = -2.1  for stack of 46-345
		Stack = -2.4  for stack of 47-344
	Helix total = -8.8
	Multiloop = 2.1  for closure of 48-343
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 287-321	Size = 2
		Stack = -3.3  for stack of 289-319
	Helix total = -3.3
	Internal/bulge = 1.1  for closure of 290-318	Size = 3
		Stack = -2.4  for stack of 292-315
		Stack = -2.4  for stack of 293-314
	Helix total = -4.8
	Internal/bulge = 2.8  for closure of 294-313	Size = 4
		Stack = -2.5  for stack of 297-310
	Helix total = -2.5
	Hairpin = 4.4  for closure of 298-309
		Stack = -1.5  for stack of 239-270
		Stack = -3.3  for stack of 240-269
		Stack = -2.4  for stack of 241-268
		Stack = -2.5  for stack of 242-267
		Stack = -1.0  for stack of 243-266
		Stack = -2.2  for stack of 244-265
		Stack = -2.1  for stack of 245-264
		Stack = -1.4  for stack of 246-263
		Stack = -0.5  for stack of 247-262
		Stack = -1.5  for stack of 248-261
	Helix total = -18.4
	Hairpin = 5.1  for closure of 249-260
		Stack = -3.4  for stack of 207-230
		Stack = -2.4  for stack of 208-229
		Stack = -3.4  for stack of 209-228
	Helix total = -9.2
	Internal/bulge = 2.8  for closure of 210-227	Size = 2
		Stack = -2.4  for stack of 213-226
		Stack = -0.6  for stack of 214-225
		Stack = -2.5  for stack of 215-224
		Stack = -3.3  for stack of 216-223
	Helix total = -8.8
	Hairpin = 2.8  for closure of 217-222
		Stack = -1.4  for stack of 158-197
		Stack = -1.4  for stack of 159-196
		Stack = -2.4  for stack of 160-195
		Stack = -3.3  for stack of 161-194
	Helix total = -8.5
	Internal/bulge = 0.5  for closure of 162-193	Size = 2
		Stack = -3.4  for stack of 164-191
		Stack = -2.4  for stack of 165-190
		Stack = -3.3  for stack of 166-189
		Stack = -2.5  for stack of 167-188
	Helix total = -11.6
	Hairpin = 6.2  for closure of 168-187
		Stack = -1.1  for stack of 120-157
		Stack = -2.1  for stack of 121-156
		Stack = -3.3  for stack of 122-155
		Stack = -3.4  for stack of 123-154
		Stack = -2.1  for stack of 124-153
	Helix total = -12.0
	Internal/bulge = 1.9  for closure of 125-152	Size = 3
		Stack = -2.1  for stack of 128-150
		Stack = -2.1  for stack of 129-149
		Stack = -2.4  for stack of 130-148
	Helix total = -6.6
	Internal/bulge = 2.3  for closure of 131-147	Size = 1 BP stack across bulge = -1.1
		Stack = -0.9  for stack of 132-145
		Stack = -1.3  for stack of 133-144
		Stack = -0.6  for stack of 134-143
		Stack = -2.5  for stack of 135-142
	Helix total = -5.3
	Hairpin = 4.1  for closure of 136-141
		Stack = -2.1  for stack of 59-87
		Stack = -1.1  for stack of 60-86
		Stack = -1.0  for stack of 61-85
		Stack = -2.1  for stack of 62-84
		Stack = -2.4  for stack of 63-83
		Stack = -2.2  for stack of 64-82
	Helix total = -10.9
	Hairpin = 4.6  for closure of 65-81


	Total energy = -108.5



