| 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 3 I | 10 3 5 | 11 3 I | 12 3 6 | 13 2 I | 14 2 7 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_92681.4_Instance_1 HL_92681.4_HL_4Y4O_164_U2528_G2535 | U | G | A | A | G | A | A | G | ||||||||||||
| HL_92681.4_Sequence_1 HL_92681.4_HL_4Y4O_164_U_2528_G_2535 | U | G | A | A | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_92681.4_Instance_2 HL_92681.4_HL_5J7L_194_U2528_G2535 | U | G | A | A | G | U | A | G | ||||||||||||
| HL_92681.4_Sequence_2 HL_92681.4_HL_5J7L_194_U_2528_G_2535 | U | G | A | A | G | U | A | G | true | 93 | 0 | 0 | 0.79 | |||||||
| HL_92681.4_Instance_3 HL_92681.4_HL_4V9F_063_U2563_G2570 | U | G | C | A | G | A | A | G | ||||||||||||
| HL_92681.4_Sequence_3 HL_92681.4_HL_4V9F_063_U_2563_G_2570 | U | G | C | A | G | A | A | G | true | 97 | 0 | 0 | 0.34 | |||||||
| HL_92681.4_Instance_4 HL_92681.4_HL_4WF9_057_U2555_G2562 | U | G | U | A | G | U | C | G | ||||||||||||
| HL_92681.4_Sequence_4 HL_92681.4_HL_4WF9_057_U_2555_G_2562 | U | G | U | A | G | U | C | G | true | 79 | 0 | 0 | 2.42 | |||||||
| HL_92681.4_Instance_5 HL_92681.4_HL_7A0S_060_U2507_G2514 | U | G | A | A | G | A | A | G | ||||||||||||
| HL_92681.4_Sequence_5 HL_92681.4_HL_7A0S_060_U_2507_G_2514 | U | G | A | A | G | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||
| HL_92681.4_Instance_6 HL_92681.4_HL_5TBW_062_A2897_U2904 | A | G | C | A | G | A | A | U | ||||||||||||
| HL_92681.4_Sequence_6 HL_92681.4_HL_5TBW_062_A_2897_U_2904 | A | G | C | A | G | A | A | U | true | 80 | 0 | 0 | 2.31 | |||||||
| HL_92681.4_Instance_7 HL_92681.4_HL_3OXE_001_G17_C24 | G | U | U | U | A | A | U | C | ||||||||||||
| HL_92681.4_Sequence_7 HL_92681.4_HL_3OXE_001_G17_C24 | G | U | U | U | A | A | U | C | true | 32 | 0 | 0 | 8.01 |
1 2 s35 1 7 cWW 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 2 6BPhJAR3D SCFG/MRF model for HL_92681.4:
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 [7] // Initial node U2528 - G2535 from junction BasepairNode | Deletion Probability [0.0000001232089072] | Pair Probability [[0.004848468,0.008566714,0.022932889,0.072045187,0.000000000],[0.065477894,0.008218312,0.113637192,0.006440127,0.000000000],[0.005770601,0.072039064,0.005210697,0.013838489,0.000000000],[0.071071676,0.006327700,0.517878680,0.005696310,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.007039775,0.985568462,0.007039775,0.000351989] | Left Letter Distribution [0.055555556,0.055555556,0.722222222,0.166666667,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [7] // Basepair U2528 - G2535 cWW HairpinNode | Num Bases [5] | Left Index [2] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A2530:A2534 Interaction | Interacting Bases [1,1] | Pair Probability [[0.388888889,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2530 Interaction | Interacting Bases [2,2] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2531 Interaction | Interacting Bases [3,3] | Pair Probability [[0.166666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G2532 Interaction | Interacting Bases [4,4] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2533 Interaction | Interacting Bases [5,5] | Pair Probability [[0.611111111,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2534Sequences of instances from HL_92681.4:
> HL_92681.4 HL_4Y4O_164 U 2528 G 2535 UGAAGAAG > HL_92681.4 HL_5J7L_194 U 2528 G 2535 UGAAGUAG > HL_92681.4 HL_4V9F_063 U 2563 G 2570 UGCAGAAG > HL_92681.4 HL_4WF9_057 U 2555 G 2562 UGUAGUCG > HL_92681.4 HL_7A0S_060 U 2507 G 2514 UGAAGAAG > HL_92681.4 HL_5TBW_062 A 2897 U 2904 AGCAGAAU > HL_92681.4 HL_3OXE_001 G 17 C 24 GUUUAAUC