Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:67 49:66 50:65 51:64 52:63 192:226 193:225 194:224
	    195:223 196:222 242:273 243:272 244:271 245:270 246:269 247:268
	    290:328 291:327 292:326 294:323 295:322 296:321
	Energy of Broken Structure: -75.4
	Energy of Pseudo-Helices:   -41.9
	Pseudoknot Energy Penalty:  32.7
	Total Free Energy:          -84.6
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-388
		Stack = -1.5  for stack of 2-387
		Stack = -2.1  for stack of 3-386
		Stack = -3.4  for stack of 4-385
		Stack = -3.3  for stack of 5-384
		Stack = -2.4  for stack of 6-383
	Helix total = -16.0
	Multiloop = 5.1  for closure of 7-382
		Stack = -3.3  for stack of 365-381
		Stack = -3.3  for stack of 366-380
		Stack = -3.3  for stack of 367-379
		Stack = -3.3  for stack of 368-378
	Helix total = -13.2
	Hairpin = 4.4  for closure of 369-377
		Stack = -2.4  for stack of 20-361
		Stack = -3.4  for stack of 21-360
		Stack = -3.3  for stack of 22-359
		Stack = -1.4  for stack of 23-358
		Stack = -2.1  for stack of 24-357
		Stack = -2.2  for stack of 25-356
		Stack = -1.3  for stack of 26-355
	Helix total = -16.1
	Internal/bulge = 4.3  for closure of 27-354	Size = 12
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 35-348	Size = 7
		Stack = -3.3  for stack of 39-343
		Stack = -2.2  for stack of 40-342
		Stack = -1.0  for stack of 41-341
	Helix total = -6.5
	Internal/bulge = 3.7  for closure of 42-340	Size = 3
		Stack = -2.1  for stack of 43-336
		Stack = -1.1  for stack of 44-335
		Stack = -2.1  for stack of 45-334
		Stack = -3.4  for stack of 46-333
	Helix total = -8.7
	Multiloop = 1.5  for closure of 47-332
		Stack = -1.1  for stack of 276-310
		Stack = -2.4  for stack of 277-309
		Stack = -3.3  for stack of 278-308
	Helix total = -6.8
	Internal/bulge = 2.2  for closure of 279-307	Size = 5
	Helix total = 0.0
	Internal/bulge = 3.4  for closure of 283-304	Size = 7
		Stack = -3.3  for stack of 287-299
		Stack = -2.1  for stack of 288-298
	Helix total = -5.4
	Hairpin = 5.7  for closure of 289-297
		Stack = -2.2  for stack of 230-258
		Stack = -2.4  for stack of 231-257
		Stack = -2.4  for stack of 232-256
		Stack = -2.5  for stack of 233-255
	Helix total = -9.5
	Internal/bulge = 0.7  for closure of 234-254	Size = 6
		Stack = -3.4  for stack of 238-250
	Helix total = -3.4
	Hairpin = 5.0  for closure of 239-249
		Stack = -2.1  for stack of 176-212
		Stack = -0.9  for stack of 177-211
		Stack = -1.1  for stack of 178-210
		Stack = -2.4  for stack of 179-209
		Stack = -2.1  for stack of 180-208
		Stack = -1.1  for stack of 181-207
	Helix total = -9.7
	Internal/bulge = 2.2  for closure of 182-206	Size = 5
		Stack = -3.3  for stack of 185-202
		Stack = -3.3  for stack of 186-201
	Helix total = -6.6
	Internal/bulge = 0.1  for closure of 187-200	Size = 4
	Helix total = 0.0
	Hairpin = 5.1  for closure of 190-197
		Stack = -2.1  for stack of 157-175
		Stack = -2.1  for stack of 158-174
		Stack = -3.3  for stack of 159-173
	Helix total = -7.5
	Internal/bulge = 1.4  for closure of 160-172	Size = 1 BP stack across bulge = -2.4
		Stack = -2.1  for stack of 162-171
		Stack = -3.4  for stack of 163-170
	Helix total = -5.5
	Hairpin = 3.7  for closure of 164-169
		Stack = -1.5  for stack of 117-156
		Stack = -2.1  for stack of 118-155
	Helix total = -3.6
	Internal/bulge = 2.3  for closure of 119-154	Size = 8
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 124-149	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 126-147	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 128-145	Size = 2
		Stack = -3.4  for stack of 130-143
		Stack = -2.1  for stack of 131-142
		Stack = -2.1  for stack of 132-141
		Stack = -3.4  for stack of 133-140
	Helix total = -11.0
	Hairpin = 3.3  for closure of 134-139
		Stack = -2.5  for stack of 55-82
		Stack = -1.0  for stack of 56-81
		Stack = -0.9  for stack of 57-80
		Stack = -2.2  for stack of 58-79
		Stack = -2.1  for stack of 59-78
		Stack = -2.1  for stack of 60-77
	Helix total = -10.8
	Hairpin = 5.8  for closure of 61-76


	Total energy = -75.4



