Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    12:360 13:359 14:358 15:357 16:356 17:355 18:354 84:296
	    85:295 86:294 87:293 88:292 89:291 90:290
	Energy of Broken Structure: -166.6
	Energy of Pseudo-Helices:   -27.2
	Pseudoknot Energy Penalty:  17.7
	Total Free Energy:          -176.1
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -0.4
		Stack = -3.3  for stack of 1-425
		Stack = -2.1  for stack of 2-424
		Stack = -2.1  for stack of 3-423
	Helix total = -7.5
	Internal/bulge = -0.6  for closure of 4-422	Size = 2
		Stack = -2.4  for stack of 6-420
		Stack = -3.3  for stack of 7-419
		Stack = -3.4  for stack of 8-418
		Stack = -3.3  for stack of 9-417
	Helix total = -12.4
	Internal/bulge = 1.4  for closure of 10-416	Size = 1 BP stack across bulge = -2.4
	Helix total = 0.0
	Multiloop = 5.2  for closure of 11-414
		Stack = -0.9  for stack of 70-412
		Stack = -2.1  for stack of 71-411
	Helix total = -3.0
	Internal/bulge = 0.4  for closure of 72-410	Size = 1 BP stack across bulge = -3.4
		Stack = -3.3  for stack of 74-409
		Stack = -2.4  for stack of 75-408
		Stack = -3.3  for stack of 76-407
		Stack = -3.3  for stack of 77-406
	Helix total = -12.3
	Multiloop = 2.7  for closure of 78-405
		Stack = -2.4  for stack of 363-395
		Stack = -2.5  for stack of 364-394
		Stack = -1.5  for stack of 365-393
		Stack = -2.4  for stack of 366-392
	Helix total = -8.8
	Internal/bulge = 0.0  for closure of 367-391	Size = 1 BP stack across bulge = -2.5
		Stack = -1.5  for stack of 368-389
		Stack = -2.4  for stack of 369-388
	Helix total = -3.9
	Internal/bulge = 1.2  for closure of 370-387	Size = 2
		Stack = -1.4  for stack of 372-385
		Stack = -2.4  for stack of 373-384
		Stack = -3.3  for stack of 374-383
		Stack = -3.3  for stack of 375-382
	Helix total = -10.4
	Hairpin = 4.2  for closure of 376-381
		Stack = -1.5  for stack of 324-343
		Stack = -2.5  for stack of 325-342
		Stack = -2.4  for stack of 326-341
		Stack = -2.5  for stack of 327-340
		Stack = -1.5  for stack of 328-339
		Stack = -3.3  for stack of 329-338
		Stack = -2.4  for stack of 330-337
	Helix total = -16.1
	Hairpin = 3.1  for closure of 331-336
		Stack = -2.4  for stack of 246-317
		Stack = -1.1  for stack of 247-316
	Helix total = -3.5
	Internal/bulge = 1.4  for closure of 248-315	Size = 1 BP stack across bulge = -2.4
	Helix total = 0.0
	Internal/bulge = 1.2  for closure of 249-313	Size = 11
		Stack = -3.3  for stack of 256-307
		Stack = -2.4  for stack of 257-306
		Stack = -2.2  for stack of 258-305
		Stack = -2.4  for stack of 259-304
		Stack = -3.3  for stack of 260-303
		Stack = -3.4  for stack of 261-302
	Helix total = -17.0
	Multiloop = 2.7  for closure of 262-301
		Stack = -3.4  for stack of 285-299
		Stack = -2.4  for stack of 286-298
	Helix total = -5.8
	Hairpin = 4.2  for closure of 287-297
		Stack = -3.4  for stack of 265-282
		Stack = -3.3  for stack of 266-281
		Stack = -3.3  for stack of 267-280
		Stack = -3.3  for stack of 268-279
		Stack = -2.4  for stack of 269-278
		Stack = -3.3  for stack of 270-277
	Helix total = -19.0
	Hairpin = 4.0  for closure of 271-276
		Stack = -2.1  for stack of 79-242
		Stack = -2.4  for stack of 80-241
		Stack = -3.3  for stack of 81-240
	Helix total = -7.8
	Internal/bulge = 4.8  for closure of 82-239	Size = 9
		Stack = -2.4  for stack of 92-238
		Stack = -3.3  for stack of 93-237
		Stack = -2.2  for stack of 94-236
		Stack = -2.1  for stack of 95-235
	Helix total = -10.0
	Multiloop = 0.2  for closure of 96-234
		Stack = -3.3  for stack of 127-233
	Helix total = -3.3
	Internal/bulge = 3.2  for closure of 128-232	Size = 3
		Stack = -2.2  for stack of 132-231
	Helix total = -2.2
	Multiloop = 4.2  for closure of 133-230
		Stack = -3.3  for stack of 201-220
		Stack = -2.1  for stack of 202-219
	Helix total = -5.4
	Internal/bulge = -1.4  for closure of 203-218	Size = 2
		Stack = -3.3  for stack of 205-216
		Stack = -3.3  for stack of 206-215
		Stack = -2.4  for stack of 207-214
	Helix total = -9.0
	Hairpin = 3.1  for closure of 208-213
		Stack = -3.3  for stack of 181-199
		Stack = -2.2  for stack of 182-198
		Stack = -2.1  for stack of 183-197
		Stack = -3.4  for stack of 184-196
		Stack = -2.4  for stack of 185-195
	Helix total = -13.4
	Hairpin = 3.8  for closure of 186-194
		Stack = -3.3  for stack of 149-173
	Helix total = -3.3
	Internal/bulge = 3.3  for closure of 150-172	Size = 2
		Stack = -2.5  for stack of 151-169
		Stack = -3.3  for stack of 152-168
		Stack = -2.4  for stack of 153-167
		Stack = -3.3  for stack of 154-166
		Stack = -3.4  for stack of 155-165
		Stack = -3.3  for stack of 156-164
	Helix total = -18.2
	Hairpin = 4.3  for closure of 157-163
	Helix total = 0.0
	Internal/bulge = 2.4  for closure of 112-126	Size = 1 BP stack across bulge = -1.4
		Stack = -2.1  for stack of 113-124
		Stack = -3.3  for stack of 114-123
		Stack = -3.3  for stack of 115-122
	Helix total = -8.7
	Hairpin = 3.1  for closure of 116-121
		Stack = -3.3  for stack of 97-111
		Stack = -2.4  for stack of 98-110
		Stack = -3.3  for stack of 99-109
		Stack = -3.3  for stack of 100-108
	Helix total = -12.3
	Hairpin = 4.6  for closure of 101-107
		Stack = -2.1  for stack of 20-65
		Stack = -1.5  for stack of 21-64
		Stack = -2.1  for stack of 22-63
		Stack = -1.5  for stack of 23-62
		Stack = -3.3  for stack of 24-61
		Stack = -2.4  for stack of 25-60
	Helix total = -12.9
	Internal/bulge = 2.9  for closure of 26-59	Size = 8
		Stack = -2.2  for stack of 32-55
		Stack = -2.4  for stack of 33-54
		Stack = -3.3  for stack of 34-53
	Helix total = -7.9
	Internal/bulge = 2.3  for closure of 35-52	Size = 3
		Stack = -2.4  for stack of 37-49
		Stack = -3.3  for stack of 38-48
		Stack = -3.3  for stack of 39-47
	Helix total = -9.0
	Hairpin = 5.0  for closure of 40-46


	Total energy = -166.6



