Pseudoknot Energy Details for Structure 1:
	Knotted Pairs:
	    18:862 19:861 20:860 456:477 457:476 458:475
	Energy of Broken Structure: -341.2
	Energy of Pseudo-Helices:   -11.9
	Pseudoknot Energy Penalty:  14.6
	Total Free Energy:          -338.5
Details follow for Broken (Pseudoknot-free) Structure.
Thermodynamic details for structure # 1
	Exterior loop = -8.7
		Stack = -1.0  for stack of 1438-1461
		Stack = -2.1  for stack of 1439-1460
		Stack = -3.3  for stack of 1440-1459
		Stack = -3.3  for stack of 1441-1458
		Stack = -3.4  for stack of 1442-1457
		Stack = -2.1  for stack of 1443-1456
		Stack = -1.0  for stack of 1444-1455
		Stack = -2.2  for stack of 1445-1454
		Stack = -2.1  for stack of 1446-1453
	Helix total = -20.5
	Hairpin = 4.7  for closure of 1447-1452
	Helix total = 0.0
	Internal/bulge = 2.3  for closure of 1331-1436	Size = 3
	Helix total = 0.0
	Internal/bulge = 2.6  for closure of 1333-1433	Size = 5
		Stack = -2.4  for stack of 1336-1429
	Helix total = -2.4
	Internal/bulge = -0.6  for closure of 1337-1428	Size = 2
	Helix total = 0.0
	Internal/bulge = 2.5  for closure of 1339-1426	Size = 3
		Stack = -2.1  for stack of 1341-1423
		Stack = -2.2  for stack of 1342-1422
		Stack = -3.3  for stack of 1343-1421
	Helix total = -7.6
	Internal/bulge = 1.2  for closure of 1344-1420	Size = 2
		Stack = -1.0  for stack of 1346-1418
		Stack = -2.1  for stack of 1347-1417
	Helix total = -3.1
	Internal/bulge = 0.8  for closure of 1348-1416	Size = 4
		Stack = -2.5  for stack of 1351-1413
		Stack = -2.1  for stack of 1352-1412
		Stack = -1.0  for stack of 1353-1411
		Stack = -2.1  for stack of 1354-1410
		Stack = -2.5  for stack of 1355-1409
		Stack = -0.5  for stack of 1356-1408
		Stack = -1.5  for stack of 1357-1407
		Stack = -2.1  for stack of 1358-1406
		Stack = -2.1  for stack of 1359-1405
		Stack = -3.4  for stack of 1360-1404
		Stack = -2.1  for stack of 1361-1403
	Helix total = -21.9
	Internal/bulge = 3.4  for closure of 1362-1402	Size = 7
	Helix total = 0.0
	Internal/bulge = 0.5  for closure of 1367-1398	Size = 2
		Stack = -2.4  for stack of 1369-1396
		Stack = -2.5  for stack of 1370-1395
		Stack = -0.5  for stack of 1371-1394
	Helix total = -5.4
	Internal/bulge = 2.3  for closure of 1372-1393	Size = 1 BP stack across bulge = -1.5
		Stack = -3.3  for stack of 1374-1392
		Stack = -3.3  for stack of 1375-1391
		Stack = -2.1  for stack of 1376-1390
	Helix total = -8.7
	Internal/bulge = 2.5  for closure of 1377-1389	Size = 3
		Stack = -3.3  for stack of 1380-1387
	Helix total = -3.3
	Hairpin = 3.7  for closure of 1381-1386
		Stack = -2.1  for stack of 865-1328
	Helix total = -2.1
	Internal/bulge = 1.4  for closure of 866-1327	Size = 1 BP stack across bulge = -2.4
		Stack = -2.2  for stack of 867-1325
		Stack = -1.4  for stack of 868-1324
	Helix total = -3.6
	Internal/bulge = 1.2  for closure of 869-1323	Size = 2
		Stack = -2.4  for stack of 871-1321
		Stack = -2.2  for stack of 872-1320
		Stack = -3.3  for stack of 873-1319
	Helix total = -7.9
	Internal/bulge = 0.8  for closure of 874-1318	Size = 1 BP stack across bulge = -2.4
	Helix total = 0.0
	Multiloop = 8.5  for closure of 875-1316
		Stack = -1.4  for stack of 1281-1304
		Stack = -1.5  for stack of 1282-1303
		Stack = -2.4  for stack of 1283-1302
		Stack = -3.4  for stack of 1284-1301
		Stack = -3.3  for stack of 1285-1300
		Stack = -2.1  for stack of 1286-1299
	Helix total = -14.1
	Hairpin = 5.3  for closure of 1287-1298
		Stack = -2.1  for stack of 880-1276
		Stack = -3.4  for stack of 881-1275
		Stack = -2.4  for stack of 882-1274
		Stack = -1.5  for stack of 883-1273
		Stack = -1.4  for stack of 884-1272
	Helix total = -10.8
	Multiloop = 6.7  for closure of 885-1271
	Helix total = 0.0
	Internal/bulge = 1.4  for closure of 1234-1265	Size = 8
		Stack = -2.1  for stack of 1239-1260
		Stack = -2.2  for stack of 1240-1259
		Stack = -1.3  for stack of 1241-1258
		Stack = -2.1  for stack of 1242-1257
		Stack = -3.3  for stack of 1243-1256
		Stack = -3.4  for stack of 1244-1255
	Helix total = -14.4
	Hairpin = 4.1  for closure of 1245-1254
		Stack = -3.3  for stack of 1173-1227
		Stack = -2.2  for stack of 1174-1226
		Stack = -0.9  for stack of 1175-1225
		Stack = -2.1  for stack of 1176-1224
		Stack = -3.3  for stack of 1177-1223
		Stack = -3.3  for stack of 1178-1222
	Helix total = -15.1
	Internal/bulge = 1.9  for closure of 1179-1221	Size = 10
		Stack = -2.1  for stack of 1185-1215
		Stack = -2.1  for stack of 1186-1214
	Helix total = -4.2
	Internal/bulge = 2.2  for closure of 1187-1213	Size = 6
		Stack = -3.4  for stack of 1190-1208
	Helix total = -3.4
	Internal/bulge = 1.5  for closure of 1191-1207	Size = 5
		Stack = -2.1  for stack of 1194-1203
		Stack = -2.4  for stack of 1195-1202
	Helix total = -4.5
	Hairpin = 3.3  for closure of 1196-1201
		Stack = -1.1  for stack of 888-1167
		Stack = -0.9  for stack of 889-1166
		Stack = -1.3  for stack of 890-1165
		Stack = -1.4  for stack of 891-1164
		Stack = -1.4  for stack of 892-1163
		Stack = -2.2  for stack of 893-1162
		Stack = -2.1  for stack of 894-1161
	Helix total = -10.4
	Internal/bulge = 0.5  for closure of 895-1160	Size = 1 BP stack across bulge = -3.3
		Stack = -2.4  for stack of 896-1158
	Helix total = -2.4
	Multiloop = 7.8  for closure of 897-1157
		Stack = -3.3  for stack of 926-1153
		Stack = -2.1  for stack of 927-1152
		Stack = -2.1  for stack of 928-1151
		Stack = -3.3  for stack of 929-1150
		Stack = -1.5  for stack of 930-1149
		Stack = -1.4  for stack of 931-1148
	Helix total = -13.7
	Multiloop = 8.3  for closure of 932-1147
		Stack = -3.3  for stack of 989-1142
	Helix total = -3.3
	Internal/bulge = 0.5  for closure of 990-1141	Size = 1 BP stack across bulge = -3.3
		Stack = -3.3  for stack of 992-1140
		Stack = -2.5  for stack of 993-1139
		Stack = 0.3  for stack of 994-1138
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 995-1137	Size = 2
		Stack = -2.1  for stack of 998-1136
	Helix total = -2.1
	Internal/bulge = 3.7  for closure of 999-1135	Size = 3
		Stack = -2.5  for stack of 1000-1131
		Stack = -2.1  for stack of 1001-1130
	Helix total = -4.6
	Internal/bulge = 1.3  for closure of 1002-1129	Size = 1 BP stack across bulge = -2.1
	Helix total = 0.0
	Internal/bulge = -0.6  for closure of 1003-1127	Size = 2
		Stack = -2.4  for stack of 1005-1125
		Stack = -2.2  for stack of 1006-1124
	Helix total = -4.6
	Multiloop = 6.1  for closure of 1007-1123
		Stack = -3.3  for stack of 1055-1119
		Stack = -2.1  for stack of 1056-1118
		Stack = -2.4  for stack of 1057-1117
		Stack = -1.4  for stack of 1058-1116
	Helix total = -9.2
	Multiloop = 8.0  for closure of 1059-1115
		Stack = -3.3  for stack of 1094-1107
		Stack = -2.1  for stack of 1095-1106
		Stack = -2.1  for stack of 1096-1105
		Stack = -2.5  for stack of 1097-1104
	Helix total = -10.0
	Hairpin = 4.7  for closure of 1098-1103
		Stack = -2.4  for stack of 1060-1088
		Stack = -2.1  for stack of 1061-1087
		Stack = -0.9  for stack of 1062-1086
		Stack = -0.9  for stack of 1063-1085
		Stack = -1.3  for stack of 1064-1084
		Stack = -2.1  for stack of 1065-1083
	Helix total = -9.7
	Internal/bulge = 2.7  for closure of 1066-1082	Size = 5
		Stack = -2.5  for stack of 1069-1078
		Stack = -3.3  for stack of 1070-1077
	Helix total = -5.8
	Hairpin = 4.1  for closure of 1071-1076
		Stack = -3.4  for stack of 1010-1049
		Stack = -2.1  for stack of 1011-1048
		Stack = -2.4  for stack of 1012-1047
		Stack = -2.4  for stack of 1013-1046
		Stack = -2.2  for stack of 1014-1045
	Helix total = -12.5
	Multiloop = 9.3  for closure of 1015-1044
		Stack = -2.1  for stack of 1030-1039
	Helix total = -2.1
	Hairpin = 3.8  for closure of 1031-1038
		Stack = -2.5  for stack of 1016-1025
		Stack = -2.1  for stack of 1017-1024
	Helix total = -4.6
	Hairpin = 4.1  for closure of 1018-1023
		Stack = -2.1  for stack of 939-986
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 940-985	Size = 1 BP stack across bulge = -2.2
		Stack = -2.4  for stack of 941-983
		Stack = -2.1  for stack of 942-982
		Stack = -0.9  for stack of 943-981
		Stack = -2.1  for stack of 944-980
	Helix total = -7.5
	Multiloop = 3.6  for closure of 945-979
		Stack = -3.3  for stack of 969-977
	Helix total = -3.3
	Hairpin = 4.6  for closure of 970-976
		Stack = -3.3  for stack of 948-965
		Stack = -2.1  for stack of 949-964
		Stack = -2.4  for stack of 950-963
		Stack = -2.1  for stack of 951-962
		Stack = -1.5  for stack of 952-961
		Stack = -2.1  for stack of 953-960
	Helix total = -13.5
	Hairpin = 4.4  for closure of 954-959
		Stack = -0.9  for stack of 902-917
		Stack = -2.4  for stack of 903-916
		Stack = -2.4  for stack of 904-915
	Helix total = -5.7
	Hairpin = 4.2  for closure of 905-914
		Stack = -2.5  for stack of 838-849
		Stack = -2.1  for stack of 839-848
		Stack = -2.4  for stack of 840-847
	Helix total = -7.0
	Hairpin = 3.3  for closure of 841-846
		Stack = -3.3  for stack of 518-827
		Stack = -3.4  for stack of 519-826
	Helix total = -6.7
	Internal/bulge = 4.0  for closure of 520-825	Size = 5
	Helix total = 0.0
	Multiloop = 3.4  for closure of 526-824
		Stack = -3.3  for stack of 773-823
		Stack = -2.4  for stack of 774-822
		Stack = -2.1  for stack of 775-821
		Stack = -2.4  for stack of 776-820
		Stack = -2.2  for stack of 777-819
		Stack = -2.1  for stack of 778-818
	Helix total = -14.5
	Multiloop = 5.3  for closure of 779-817
		Stack = -3.4  for stack of 805-812
	Helix total = -3.4
	Hairpin = 4.2  for closure of 806-811
		Stack = -2.1  for stack of 781-801
		Stack = -2.5  for stack of 782-800
		Stack = 0.3  for stack of 783-799
		Stack = -2.5  for stack of 784-798
		Stack = -2.1  for stack of 785-797
		Stack = -2.1  for stack of 786-796
		Stack = -3.4  for stack of 787-795
	Helix total = -14.4
	Hairpin = 4.7  for closure of 788-794
		Stack = -3.4  for stack of 721-762
		Stack = -2.1  for stack of 722-761
		Stack = -2.1  for stack of 723-760
		Stack = -3.3  for stack of 724-759
		Stack = -3.3  for stack of 725-758
		Stack = -1.5  for stack of 726-757
	Helix total = -15.7
	Internal/bulge = 3.7  for closure of 727-756	Size = 3
	Helix total = 0.0
	Internal/bulge = 0.7  for closure of 731-755	Size = 6
		Stack = -1.3  for stack of 735-751
		Stack = -2.1  for stack of 736-750
		Stack = -3.3  for stack of 737-749
	Helix total = -6.7
	Hairpin = 4.9  for closure of 738-748
		Stack = -2.2  for stack of 528-716
		Stack = -2.4  for stack of 529-715
		Stack = -2.1  for stack of 530-714
	Helix total = -6.7
	Internal/bulge = 1.4  for closure of 531-713	Size = 6
		Stack = -2.1  for stack of 535-709
		Stack = -2.2  for stack of 536-708
		Stack = -2.1  for stack of 537-707
	Helix total = -6.4
	Multiloop = 5.3  for closure of 538-706
		Stack = -2.1  for stack of 607-703
		Stack = -2.2  for stack of 608-702
	Helix total = -4.3
	Internal/bulge = 3.0  for closure of 609-701	Size = 3
		Stack = -2.4  for stack of 611-698
		Stack = -3.3  for stack of 612-697
		Stack = -2.5  for stack of 613-696
	Helix total = -8.2
	Internal/bulge = 2.8  for closure of 614-695	Size = 5
		Stack = -2.1  for stack of 618-692
		Stack = -3.4  for stack of 619-691
		Stack = -2.1  for stack of 620-690
		Stack = -2.1  for stack of 621-689
		Stack = -2.4  for stack of 622-688
		Stack = -2.1  for stack of 623-687
	Helix total = -14.2
	Multiloop = 3.8  for closure of 624-686
		Stack = -3.4  for stack of 677-684
	Helix total = -3.4
	Hairpin = 3.2  for closure of 678-683
	Helix total = 0.0
	Internal/bulge = 0.7  for closure of 625-669	Size = 6
		Stack = -0.6  for stack of 629-665
		Stack = -2.4  for stack of 630-664
		Stack = -3.3  for stack of 631-663
		Stack = -2.1  for stack of 632-662
		Stack = -1.1  for stack of 633-661
		Stack = -1.0  for stack of 634-660
		Stack = -1.4  for stack of 635-659
	Helix total = -11.9
	Internal/bulge = 2.9  for closure of 636-658	Size = 9
		Stack = -3.4  for stack of 640-651
		Stack = -1.4  for stack of 641-650
	Helix total = -4.8
	Hairpin = 4.4  for closure of 642-649
		Stack = -3.4  for stack of 539-603
		Stack = -2.1  for stack of 540-602
		Stack = -2.4  for stack of 541-601
		Stack = -2.4  for stack of 542-600
		Stack = -2.2  for stack of 543-599
	Helix total = -12.5
	Internal/bulge = 3.7  for closure of 544-598	Size = 3
		Stack = -2.1  for stack of 547-596
	Helix total = -2.1
	Internal/bulge = 3.7  for closure of 548-595	Size = 3
		Stack = -2.4  for stack of 549-591
		Stack = -2.1  for stack of 550-590
		Stack = -1.0  for stack of 551-589
		Stack = -0.9  for stack of 552-588
		Stack = -1.1  for stack of 553-587
		Stack = -2.1  for stack of 554-586
		Stack = -2.5  for stack of 555-585
		Stack = -1.5  for stack of 556-584
	Helix total = -13.6
	Internal/bulge = 3.5  for closure of 557-583	Size = 8
		Stack = -3.3  for stack of 563-579
		Stack = -2.1  for stack of 564-578
		Stack = -0.6  for stack of 565-577
		Stack = -2.1  for stack of 566-576
		Stack = -3.3  for stack of 567-575
	Helix total = -11.4
	Hairpin = 4.6  for closure of 568-574
		Stack = -3.3  for stack of 28-507
		Stack = -2.4  for stack of 29-506
		Stack = -2.2  for stack of 30-505
	Helix total = -7.9
	Internal/bulge = 1.7  for closure of 31-504	Size = 1 BP stack across bulge = -2.1
		Stack = -0.9  for stack of 33-503
		Stack = -2.2  for stack of 34-502
		Stack = -2.4  for stack of 35-501
		Stack = -3.4  for stack of 36-500
		Stack = -2.1  for stack of 37-499
	Helix total = -11.0
	Multiloop = 2.2  for closure of 38-498
		Stack = -3.4  for stack of 451-496
		Stack = -2.1  for stack of 452-495
		Stack = -2.2  for stack of 453-494
		Stack = -3.3  for stack of 454-493
	Helix total = -11.0
	Internal/bulge = 4.4  for closure of 455-492	Size = 6
		Stack = -2.1  for stack of 462-491
		Stack = -2.4  for stack of 463-490
		Stack = -2.1  for stack of 464-489
		Stack = -2.1  for stack of 465-488
	Helix total = -8.7
	Hairpin = 6.1  for closure of 466-487
		Stack = -2.4  for stack of 416-443
		Stack = -2.1  for stack of 417-442
		Stack = -2.1  for stack of 418-441
		Stack = -2.4  for stack of 419-440
	Helix total = -9.0
	Internal/bulge = 1.4  for closure of 420-439	Size = 7
	Helix total = 0.0
	Hairpin = 5.3  for closure of 424-434
		Stack = -3.4  for stack of 380-410
		Stack = -2.1  for stack of 381-409
		Stack = -2.1  for stack of 382-408
	Helix total = -7.6
	Internal/bulge = 1.2  for closure of 383-407	Size = 11
		Stack = -1.5  for stack of 390-401
		Stack = -2.5  for stack of 391-400
		Stack = -3.3  for stack of 392-399
	Helix total = -7.3
	Hairpin = 4.6  for closure of 393-398
		Stack = -3.4  for stack of 40-377
		Stack = -2.4  for stack of 41-376
		Stack = -3.3  for stack of 42-375
		Stack = -3.4  for stack of 43-374
		Stack = -2.1  for stack of 44-373
	Helix total = -14.6
	Internal/bulge = 2.3  for closure of 45-372	Size = 1 BP stack across bulge = -1.1
		Stack = -2.1  for stack of 46-370
	Helix total = -2.1
	Multiloop = 5.2  for closure of 47-369
	Helix total = 0.0
	Internal/bulge = 1.6  for closure of 343-367	Size = 1 BP stack across bulge = -1.3
		Stack = -1.5  for stack of 345-366
		Stack = -2.4  for stack of 346-365
	Helix total = -3.9
	Internal/bulge = 3.0  for closure of 347-364	Size = 4
	Helix total = 0.0
	Internal/bulge = 3.3  for closure of 351-362	Size = 2
		Stack = -3.4  for stack of 354-361
	Helix total = -3.4
	Hairpin = 3.3  for closure of 355-360
	Helix total = 0.0
	Internal/bulge = 3.8  for closure of 48-337	Size = 5
		Stack = -2.1  for stack of 53-335
		Stack = -2.2  for stack of 54-334
	Helix total = -4.3
	Internal/bulge = 1.7  for closure of 55-333	Size = 1 BP stack across bulge = -2.1
		Stack = -2.1  for stack of 57-332
		Stack = -3.4  for stack of 58-331
	Helix total = -5.5
	Multiloop = -0.3  for closure of 59-330
		Stack = -2.1  for stack of 315-326
		Stack = -2.4  for stack of 316-325
		Stack = -3.3  for stack of 317-324
	Helix total = -7.8
	Hairpin = 2.8  for closure of 318-323
		Stack = -2.1  for stack of 292-313
		Stack = -2.1  for stack of 293-312
		Stack = -3.3  for stack of 294-311
		Stack = -3.3  for stack of 295-310
	Helix total = -10.8
	Hairpin = 5.4  for closure of 296-309
		Stack = -2.2  for stack of 99-290
		Stack = -2.1  for stack of 100-289
	Helix total = -4.3
	Multiloop = 4.4  for closure of 101-288
		Stack = -3.4  for stack of 265-287
		Stack = -2.1  for stack of 266-286
		Stack = -2.1  for stack of 267-285
	Helix total = -7.6
	Internal/bulge = 3.7  for closure of 268-284	Size = 3
		Stack = -1.4  for stack of 269-280
		Stack = -2.4  for stack of 270-279
		Stack = -2.1  for stack of 271-278
	Helix total = -5.9
	Hairpin = 4.7  for closure of 272-277
		Stack = -2.1  for stack of 215-262
		Stack = -2.1  for stack of 216-261
	Helix total = -4.2
	Internal/bulge = 2.9  for closure of 217-260	Size = 10
		Stack = -3.4  for stack of 222-253
		Stack = -2.1  for stack of 223-252
	Helix total = -5.5
	Internal/bulge = 3.8  for closure of 224-251	Size = 2
		Stack = -0.9  for stack of 227-250
		Stack = -2.1  for stack of 228-249
		Stack = -3.3  for stack of 229-248
	Helix total = -6.3
	Internal/bulge = 1.2  for closure of 230-247	Size = 2
		Stack = -2.1  for stack of 232-245
		Stack = -3.3  for stack of 233-244
	Helix total = -5.4
	Hairpin = 3.3  for closure of 234-243
		Stack = -2.5  for stack of 108-214
		Stack = -2.4  for stack of 109-213
		Stack = -2.5  for stack of 110-212
		Stack = -1.0  for stack of 111-211
		Stack = -0.9  for stack of 112-210
		Stack = -2.1  for stack of 113-209
	Helix total = -11.4
	Internal/bulge = 1.1  for closure of 114-208	Size = 3
		Stack = -3.3  for stack of 117-206
	Helix total = -3.3
	Internal/bulge = 2.6  for closure of 118-205	Size = 5
		Stack = -2.1  for stack of 122-202
		Stack = -1.3  for stack of 123-201
		Stack = -1.1  for stack of 124-200
		Stack = -2.4  for stack of 125-199
		Stack = -2.4  for stack of 126-198
		Stack = -3.3  for stack of 127-197
	Helix total = -12.6
	Multiloop = 3.5  for closure of 128-196
		Stack = -3.3  for stack of 184-194
		Stack = -2.2  for stack of 185-193
	Helix total = -5.5
	Hairpin = 4.2  for closure of 186-192
		Stack = -2.5  for stack of 170-179
		Stack = -2.1  for stack of 171-178
	Helix total = -4.6
	Hairpin = 4.1  for closure of 172-177
		Stack = -3.3  for stack of 130-164
		Stack = -3.3  for stack of 131-163
		Stack = -3.3  for stack of 132-162
	Helix total = -9.9
	Internal/bulge = 2.2  for closure of 133-161	Size = 11
		Stack = -2.1  for stack of 139-154
	Helix total = -2.1
	Internal/bulge = 1.2  for closure of 140-153	Size = 2
		Stack = 0.3  for stack of 142-151
		Stack = -2.1  for stack of 143-150
	Helix total = -1.8
	Hairpin = 3.1  for closure of 144-149
		Stack = -2.5  for stack of 62-92
		Stack = -1.5  for stack of 63-91
	Helix total = -4.0
	Internal/bulge = 3.3  for closure of 64-90	Size = 2
		Stack = -2.2  for stack of 67-89
	Helix total = -2.2
	Internal/bulge = 1.1  for closure of 68-88	Size = 5
		Stack = -2.5  for stack of 71-84
		Stack = -2.1  for stack of 72-83
		Stack = -0.9  for stack of 73-82
		Stack = -0.9  for stack of 74-81
	Helix total = -6.4
	Hairpin = 4.4  for closure of 75-80
		Stack = -2.4  for stack of 10-26
		Stack = -2.1  for stack of 11-25
		Stack = -2.5  for stack of 12-24
		Stack = -0.5  for stack of 13-23
	Helix total = -7.5
	Hairpin = 5.1  for closure of 14-22


	Total energy = -341.2



