| 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 7 2 | 5 7 I | 6 8 3 | 7 8 I | 8 8 4 | 9 8 I | 10 8 5 | 11 8 I | 12 8 6 | 13 7 I | 14 7 7 | 15 6 I | 16 5 8 | 17 4 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_23537.2_Instance_1 HL_23537.2_HL_4OJI_002_G23_C32 | G | U | C | C | C | A | A | G | C | C | ||||||||||||||||
| HL_23537.2_Sequence_1 HL_23537.2_HL_4OJI_002_G23_C32 | G | U | C | C | C | A | A | G | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| HL_23537.2_Instance_2 HL_23537.2_HL_4RGE_003_G29_C38 | G | U | C | C | U | A | A | G | C | C | ||||||||||||||||
| HL_23537.2_Sequence_2 HL_23537.2_HL_4RGE_003_G29_C38 | G | U | C | C | U | A | A | G | C | C | true | 97 | 0 | 0 | 0.51 | |||||||||||
| HL_23537.2_Instance_3 HL_23537.2_HL_4QJD_004_G43_C52 | G | U | C | C | C | A | A | G | C | C | ||||||||||||||||
| HL_23537.2_Sequence_3 HL_23537.2_HL_4QJD_004_G43_C52 | G | U | C | C | C | A | A | G | C | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 10 cWW 2 7 tWH 3 4 s35 4 5 s35 5 6 s33 7 10 s35 8 9 s35 10 9 7BPhJAR3D SCFG/MRF model for HL_23537.2:
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 [10] // Initial node G23 - C32 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G23 - C32 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.700000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.100000000,0.700000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.017707924,0.003918792,0.018392577,0.003918792,0.000000000],[0.039408615,0.315779730,0.003918792,0.003918792,0.000000000],[0.003918792,0.009393603,0.029802081,0.017429436,0.000000000],[0.467237476,0.003918792,0.022736360,0.038599448,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U24 - A29 tWH HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [0.999999999999999] // Hairpin node C25:A28 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C25 Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C26 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C27 Interaction | Interacting Bases [4,4] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A28Sequences of instances from HL_23537.2:
> HL_23537.2 HL_4OJI_002 G 23 C 32 GUCCCAAGCC > HL_23537.2 HL_4RGE_003 G 29 C 38 GUCCUAAGCC > HL_23537.2 HL_4QJD_004 G 43 C 52 GUCCCAAGCC