Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    48:68 49:67 50:66 51:65 52:64 176:206 177:205 179:203
	    221:257 222:256 223:255 224:254 225:253 226:252 227:251 273:311
	    274:310 275:309 276:308 277:307 278:306 281:303
	Energy of Broken Structure: -107.2
	Energy of Pseudo-Helices:   -38.7
	Pseudoknot Energy Penalty:  35.5
	Total Free Energy:          -110.4
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -1.7
		Stack = -3.3  for stack of 1-371
		Stack = -1.5  for stack of 2-370
		Stack = -2.1  for stack of 3-369
		Stack = -3.3  for stack of 4-368
		Stack = -2.2  for stack of 5-367
		Stack = -2.1  for stack of 6-366
	Helix total = -14.5
	Multiloop = 5.0  for closure of 7-365
		Stack = -3.4  for stack of 348-364
		Stack = -2.4  for stack of 349-363
		Stack = -3.3  for stack of 350-362
		Stack = -3.3  for stack of 351-361
	Helix total = -12.4
	Hairpin = 4.4  for closure of 352-360
		Stack = -2.1  for stack of 19-344
		Stack = -2.4  for stack of 20-343
		Stack = -3.3  for stack of 21-342
		Stack = -2.4  for stack of 22-341
		Stack = -3.3  for stack of 23-340
	Helix total = -13.5
	Internal/bulge = 0.5  for closure of 24-339	Size = 2
	Helix total = 0.0
	Internal/bulge = -1.4  for closure of 26-337	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 28-335	Size = 1 BP stack across bulge = -1.4
		Stack = -2.4  for stack of 30-334
	Helix total = -2.4
	Internal/bulge = -0.7  for closure of 31-333	Size = 2
		Stack = -2.5  for stack of 33-331
		Stack = -2.1  for stack of 34-330
		Stack = -2.1  for stack of 35-329
		Stack = -3.3  for stack of 36-328
		Stack = -3.3  for stack of 37-327
	Helix total = -13.3
	Internal/bulge = 1.7  for closure of 38-326	Size = 10
		Stack = -2.4  for stack of 43-319
		Stack = -3.3  for stack of 44-318
		Stack = -3.3  for stack of 45-317
		Stack = -3.4  for stack of 46-316
	Helix total = -12.4
	Multiloop = 4.3  for closure of 47-315
		Stack = -2.1  for stack of 258-293
		Stack = -3.4  for stack of 259-292
		Stack = -3.3  for stack of 260-291
		Stack = -2.1  for stack of 261-290
	Helix total = -10.9
	Internal/bulge = 2.3  for closure of 262-289	Size = 1 BP stack across bulge = -1.5
		Stack = -2.4  for stack of 264-288
		Stack = -3.4  for stack of 265-287
		Stack = -3.3  for stack of 266-286
		Stack = -2.4  for stack of 267-285
		Stack = -3.3  for stack of 268-284
	Helix total = -14.8
	Hairpin = 5.7  for closure of 269-283
		Stack = -3.3  for stack of 211-239
		Stack = -2.4  for stack of 212-238
	Helix total = -5.7
	Internal/bulge = -0.6  for closure of 213-237	Size = 2
		Stack = -3.3  for stack of 215-235
	Helix total = -3.3
	Internal/bulge = 1.2  for closure of 216-234	Size = 2
		Stack = -2.2  for stack of 218-232
		Stack = -3.3  for stack of 219-231
	Helix total = -5.5
	Hairpin = 5.4  for closure of 220-230
		Stack = -2.4  for stack of 159-195
		Stack = -2.5  for stack of 160-194
		Stack = -1.5  for stack of 161-193
		Stack = -2.1  for stack of 162-192
		Stack = -2.1  for stack of 163-191
	Helix total = -10.6
	Internal/bulge = 2.3  for closure of 164-190	Size = 4
		Stack = -2.1  for stack of 166-186
		Stack = -2.1  for stack of 167-185
		Stack = -3.3  for stack of 168-184
		Stack = -3.3  for stack of 169-183
	Helix total = -10.8
	Hairpin = 5.3  for closure of 170-182
		Stack = -2.1  for stack of 118-148
		Stack = -2.4  for stack of 119-147
	Helix total = -4.5
	Internal/bulge = 1.2  for closure of 120-146	Size = 2
		Stack = -2.2  for stack of 122-144
		Stack = -2.1  for stack of 123-143
		Stack = -1.3  for stack of 124-142
	Helix total = -5.6
	Internal/bulge = 2.2  for closure of 125-141	Size = 4
		Stack = -3.4  for stack of 128-138
		Stack = -3.3  for stack of 129-137
	Helix total = -6.7
	Hairpin = 4.6  for closure of 130-136
		Stack = -2.1  for stack of 54-83
		Stack = -2.4  for stack of 55-82
		Stack = -0.6  for stack of 56-81
		Stack = -2.5  for stack of 57-80
		Stack = -2.4  for stack of 58-79
	Helix total = -10.0
	Hairpin = 5.6  for closure of 59-78


	Total energy = -107.2



