Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    50:68 51:67 52:66 53:65 54:64 178:224 179:223 180:222
	    181:221 183:220 239:268 240:267 241:266 242:265 243:264 244:263
	    285:325 286:324 287:323 288:322 290:320 291:319 292:318
	Energy of Broken Structure: -37.8
	Energy of Pseudo-Helices:   -37.5
	Pseudoknot Energy Penalty:  31.5
	Total Free Energy:          -43.8
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 = -2.1  for stack of 5-384
		Stack = -2.1  for stack of 6-383
	Helix total = -14.5
	Multiloop = 5.2  for closure of 7-382
		Stack = -3.4  for stack of 365-381
		Stack = -2.4  for stack of 366-380
		Stack = -3.3  for stack of 367-379
		Stack = -3.3  for stack of 368-378
	Helix total = -12.4
	Hairpin = 5.0  for closure of 369-377
		Stack = -1.4  for stack of 21-361
		Stack = -2.1  for stack of 22-360
		Stack = -2.4  for stack of 23-359
		Stack = -0.6  for stack of 24-358
		Stack = -1.4  for stack of 25-357
	Helix total = -7.9
	Internal/bulge = 1.9  for closure of 26-356	Size = 2
	Helix total = 0.0
	Internal/bulge = 1.9  for closure of 28-354	Size = 2
	Helix total = 0.0
	Internal/bulge = 4.0  for closure of 30-352	Size = 5
		Stack = -1.3  for stack of 34-349
		Stack = -1.1  for stack of 35-348
		Stack = -0.9  for stack of 36-347
		Stack = -0.9  for stack of 37-346
	Helix total = -4.2
	Internal/bulge = 2.8  for closure of 38-345	Size = 4
		Stack = -2.1  for stack of 41-342
		Stack = -2.2  for stack of 42-341
		Stack = -1.0  for stack of 43-340
	Helix total = -5.3
	Internal/bulge = 4.5  for closure of 44-339	Size = 5
		Stack = -2.1  for stack of 45-333
		Stack = -1.1  for stack of 46-332
		Stack = -2.1  for stack of 47-331
		Stack = -3.4  for stack of 48-330
	Helix total = -8.7
	Multiloop = 5.3  for closure of 49-329
		Stack = -1.4  for stack of 271-307
		Stack = -0.9  for stack of 272-306
		Stack = -2.1  for stack of 273-305
		Stack = -3.3  for stack of 274-304
	Helix total = -7.7
	Internal/bulge = 0.9  for closure of 275-303	Size = 1 BP stack across bulge = -2.5
	Helix total = 0.0
	Internal/bulge = 4.3  for closure of 277-302	Size = 10
		Stack = -1.1  for stack of 282-295
	Helix total = -1.1
	Hairpin = 5.6  for closure of 283-294
		Stack = -2.5  for stack of 227-254
		Stack = -2.4  for stack of 228-253
		Stack = -2.2  for stack of 229-252
	Helix total = -7.1
	Internal/bulge = 1.9  for closure of 230-251	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.2  for closure of 232-249	Size = 3
		Stack = -3.4  for stack of 235-247
		Stack = -2.1  for stack of 236-246
	Helix total = -5.5
	Hairpin = 5.1  for closure of 237-245
		Stack = -3.3  for stack of 160-208
		Stack = -2.1  for stack of 161-207
		Stack = -2.4  for stack of 162-206
		Stack = -2.1  for stack of 163-205
		Stack = -2.4  for stack of 164-204
	Helix total = -12.3
	Internal/bulge = 6.1  for closure of 165-203	Size = 9
		Stack = -0.9  for stack of 167-194
		Stack = -0.9  for stack of 168-193
	Helix total = -1.8
	Internal/bulge = 1.9  for closure of 169-192	Size = 2
		Stack = -0.9  for stack of 171-190
		Stack = -1.1  for stack of 172-189
		Stack = -1.3  for stack of 173-188
		Stack = -1.1  for stack of 174-187
		Stack = -1.3  for stack of 175-186
	Helix total = -5.7
	Hairpin = 5.3  for closure of 176-185
		Stack = -2.4  for stack of 112-159
		Stack = -0.9  for stack of 113-158
		Stack = -1.4  for stack of 114-157
		Stack = -1.5  for stack of 115-156
		Stack = -2.1  for stack of 116-155
	Helix total = -8.3
	Internal/bulge = 3.8  for closure of 117-154	Size = 2
	Helix total = 0.0
	Internal/bulge = 3.1  for closure of 118-151	Size = 4
	Helix total = 0.0
	Internal/bulge = 2.0  for closure of 121-148	Size = 4
		Stack = -0.9  for stack of 124-145
		Stack = -1.3  for stack of 125-144
		Stack = -2.1  for stack of 126-143
	Helix total = -4.3
	Hairpin = 5.8  for closure of 127-142
		Stack = -2.1  for stack of 55-80
		Stack = -2.4  for stack of 56-79
		Stack = -2.1  for stack of 57-78
		Stack = -3.3  for stack of 58-77
		Stack = -3.4  for stack of 59-76
	Helix total = -13.3
	Hairpin = 5.4  for closure of 60-75


	Total energy = -37.8



