| Column number: Node in JAR3D model: Insertion positions indicated by I: Position in motif group: | 1 1 I | 2 2 1 | 3 2 I | 4 3 2 | 5 3 I | 6 3 3 | 7 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_86880.4_Instance_1 HL_86880.4_HL_4WF9_033_G1361_C1367 | G | C | U | C | G | U | C | |||||||||
| HL_86880.4_Sequence_1 HL_86880.4_HL_4WF9_033_G_1361_C_1367 | G | C | U | C | G | U | C | true | 100 | 0 | 0 | 0.00 | ||||
| HL_86880.4_Instance_2 HL_86880.4_HL_4Y4O_135_G1324_C1330 | G | G | U | C | G | U | C | |||||||||
| HL_86880.4_Sequence_2 HL_86880.4_HL_4Y4O_135_G_1324_C_1330 | G | G | U | C | G | U | C | true | 97 | 0 | 0 | 0.25 | ||||
| HL_86880.4_Instance_3 HL_86880.4_HL_7A0S_033_G1337_C1343 | G | G | U | C | G | U | C | |||||||||
| HL_86880.4_Sequence_3 HL_86880.4_HL_7A0S_033_G_1337_C_1343 | G | G | U | C | G | U | C | true | 97 | 0 | 0 | 0.25 | ||||
| HL_86880.4_Instance_4 HL_86880.4_HL_4V9F_035_G1430_C1436 | G | C | U | G | A | U | C | |||||||||
| HL_86880.4_Sequence_4 HL_86880.4_HL_4V9F_035_G_1430_C_1436 | G | C | U | G | A | U | C | true | 78 | 0 | 0 | 2.10 | ||||
| HL_86880.4_Instance_5 HL_86880.4_HL_5J7L_170_G1492_C1498 | G | C | A | A | A | U | C | |||||||||
| HL_86880.4_Sequence_5 HL_86880.4_HL_5J7L_170_G_1492_C_1498 | G | C | A | A | A | U | C | true | 93 | 0 | 0 | 0.64 | ||||
| HL_86880.4_Instance_6 HL_86880.4_HL_5TBW_032_A1506_U1512 | A | G | C | A | G | U | U | |||||||||
| HL_86880.4_Sequence_6 HL_86880.4_HL_5TBW_032_A_1506_U_1512 | A | G | C | A | G | U | U | true | 78 | 0 | 0 | 2.09 | ||||
| HL_86880.4_Instance_7 HL_86880.4_HL_4Y4O_139_G1492_C1498 | G | C | A | A | A | U | C | |||||||||
| HL_86880.4_Sequence_7 HL_86880.4_HL_4Y4O_139_G_1492_C_1498 | G | C | A | A | A | U | C | true | 93 | 0 | 0 | 0.64 | ||||
| HL_86880.4_Instance_8 HL_86880.4_HL_5J7L_166_G1324_C1330 | G | U | U | A | A | U | C | |||||||||
| HL_86880.4_Sequence_8 HL_86880.4_HL_5J7L_166_G_1324_C_1330 | G | U | U | A | A | U | C | true | 80 | 0 | 0 | 1.90 | ||||
| HL_86880.4_Instance_9 HL_86880.4_HL_5VJ9_003_G6_C11 | G | A | C | G | A | C | ||||||||||
| HL_86880.4_Sequence_9 HL_86880.4_HL_5VJ9_003_G6_C11 | G | A | C | G | A | C | true | 96 | 0 | 0 | 0.36 | |||||
| HL_86880.4_Instance_10 HL_86880.4_HL_5NDI_002_G8_C13 | G | A | C | G | A | C | ||||||||||
| HL_86880.4_Sequence_10 HL_86880.4_HL_5NDI_002_G8_C13 | G | A | C | G | A | C | true | 96 | 0 | 0 | 0.36 | |||||
| HL_86880.4_Instance_11 HL_86880.4_HL_5NDH_001_G6_C11 | G | A | C | G | A | C | ||||||||||
| HL_86880.4_Sequence_11 HL_86880.4_HL_5NDH_001_G6_C11 | G | A | C | G | A | C | true | 96 | 0 | 0 | 0.36 | |||||
| HL_86880.4_Instance_12 HL_86880.4_HL_4Y4O_143_C1631_G1635 | C | A | A | G | A | G | ||||||||||
| HL_86880.4_Sequence_12 HL_86880.4_HL_4Y4O_143_C_1631_G_1635 | C | A | A | G | A | G | true | 91 | 0 | 0 | 0.89 |
1 4 s33 1 5 cWW 2 3 s35 3 4 s35 4 5 s35JAR3D SCFG/MRF model for HL_86880.4:
Character Definition | A,C,G,U,* // Define characters here InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Initial node G1361 - C1367 from junction BasepairNode | Deletion Probability [0.0000000035949991] | Pair Probability [[0.008815443,0.018353160,0.009996502,0.192294218,0.000000000],[0.015844115,0.008708069,0.193606842,0.011914381,0.000000000],[0.009910961,0.278185774,0.001899121,0.026132318,0.000000000],[0.180991745,0.012309084,0.021583371,0.009454896,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.333724057,0.663311039,0.002827001,0.000137903] | Left Letter Distribution [0.050000000,0.450000000,0.350000000,0.150000000,0.000000000] | Right Length Distribution [0.004131378,0.991530675,0.004131378,0.000206569] | Right Letter Distribution [0.321428571,0.035714286,0.035714286,0.607142857,0.000000000] | Left Index [1] | Right Index [5] // Basepair G1361 - C1367 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U1363:G1365 Interaction | Interacting Bases [1,1] | Pair Probability [[0.464285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.107142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.392857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U1363 Interaction | Interacting Bases [2,2] | Pair Probability [[0.392857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.464285714,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.107142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1364 Interaction | Interacting Bases [3,3] | Pair Probability [[0.321428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.607142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1365Sequences of instances from HL_86880.4:
> HL_86880.4 HL_4WF9_033 G 1361 C 1367 GCUCGUC > HL_86880.4 HL_4Y4O_135 G 1324 C 1330 GGUCGUC > HL_86880.4 HL_7A0S_033 G 1337 C 1343 GGUCGUC > HL_86880.4 HL_4V9F_035 G 1430 C 1436 GCUGAUC > HL_86880.4 HL_5J7L_170 G 1492 C 1498 GCAAAUC > HL_86880.4 HL_5TBW_032 A 1506 U 1512 AGCAGUU > HL_86880.4 HL_4Y4O_139 G 1492 C 1498 GCAAAUC > HL_86880.4 HL_5J7L_166 G 1324 C 1330 GUUAAUC > HL_86880.4 HL_5VJ9_003 G 6 C 11 GACGAC > HL_86880.4 HL_5NDI_002 G 8 C 13 GACGAC > HL_86880.4 HL_5NDH_001 G 6 C 11 GACGAC > HL_86880.4 HL_4Y4O_143 C 1631 G 1635 CAAGAG