| 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 4 3 | 7 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 4 I | 14 4 7 | 15 3 I | 16 3 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_32735.2_Instance_1 HL_32735.2,HL_5J7L_193,A2471_U2479 | A | G | U | U | C | A | U | A | U | |||||||||||||||
| HL_32735.2_Sequence_1 HL_32735.25J7L_A_2471_U_2479 | A | G | U | U | C | A | U | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_32735.2_Instance_2 HL_32735.2,HL_8P9A_172,C2840_G2848 | C | G | U | U | C | A | U | A | G | |||||||||||||||
| HL_32735.2_Sequence_2 HL_32735.28P9A_C_2840_G_2848 | C | G | U | U | C | A | U | A | G | true | 100 | 0 | 0 | 0.03 | ||||||||||
| HL_32735.2_Instance_3 HL_32735.2,HL_4WF9_056,A2498_U2506 | A | G | U | U | C | A | C | A | U | |||||||||||||||
| HL_32735.2_Sequence_3 HL_32735.24WF9_A_2498_U_2506 | A | G | U | U | C | A | C | A | U | true | 95 | 0 | 0 | 0.79 | ||||||||||
| HL_32735.2_Instance_4 HL_32735.2,HL_9DFE_058,C2471_G2479 | C | G | U | C | C | A | C | A | G | |||||||||||||||
| HL_32735.2_Sequence_4 HL_32735.29DFE_C_2471_G_2479 | C | G | U | C | C | A | C | A | G | true | 91 | 0 | 0 | 1.49 | ||||||||||
| HL_32735.2_Instance_5 HL_32735.2,HL_7A0S_059,A2450_U2458 | A | G | U | C | C | A | U | A | U | |||||||||||||||
| HL_32735.2_Sequence_5 HL_32735.27A0S_A_2450_U_2458 | A | G | U | C | C | A | U | A | U | true | 96 | 0 | 0 | 0.68 | ||||||||||
| HL_32735.2_Instance_6 HL_32735.2,HL_8CRE_060,C2812_G2820 | C | G | U | U | C | A | U | A | G | |||||||||||||||
| HL_32735.2_Sequence_6 HL_32735.28CRE_C_2812_G_2820 | C | G | U | U | C | A | U | A | G | true | 100 | 0 | 0 | 0.03 | ||||||||||
| HL_32735.2_Instance_7 HL_32735.2,HL_4V9F_062,A2506_U2514 | A | G | C | A | C | A | U | A | U | |||||||||||||||
| HL_32735.2_Sequence_7 HL_32735.24V9F_A_2506_U_2514 | A | G | C | A | C | A | U | A | U | true | 83 | 0 | 0 | 2.80 |
1 2 s35 1 9 cWW 2 5 s33 2 8 tSH 3 4 s35 4 5 s35 6 7 s35 8 9 s35 4 3 7BPh 5 3 6BPh 5 4 7BPh 2 7 6BPh 8 2 6BR 1 6 7BRJAR3D SCFG/MRF model for HL_32735.2:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [9] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012659138,0.028907456,0.013676753,0.313542328,0.000000000],[0.026353506,0.013028373,0.304280523,0.017394334,0.000000000],[0.005597740,0.107787255,0.001115040,0.022831626,0.000000000],[0.107219597,0.006425973,0.013217095,0.005963263,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | 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 [9] // Basepair A2471 - U2479 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.041656033,0.044098525,0.000500053,0.002356751,0.000000000],[0.041965507,0.043996411,0.000500053,0.000500053,0.000000000],[0.415457595,0.003500370,0.017112199,0.297098200,0.000000000],[0.046499257,0.043758888,0.000500053,0.000500053,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair G2472 - A2478 tSH HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U2473:U2477 Interaction | Interacting Bases [1,1] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.722222222,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2473 Interaction | Interacting Bases [2,2] | Pair Probability [[0.147058824,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.284313725,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.558823529,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2474 Interaction | Interacting Bases [3,3] | Pair Probability [[0.001449275,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.995652174,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.001449275,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.001449275,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2475 Interaction | Interacting Bases [4,4] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2476 Interaction | Interacting Bases [5,5] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.611111111,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2477Sequences of instances from HL_32735.2:
> HL_32735.2 5J7L A 2471 U 2479 AGUUCAUAU > HL_32735.2 8P9A C 2840 G 2848 CGUUCAUAG > HL_32735.2 4WF9 A 2498 U 2506 AGUUCACAU > HL_32735.2 9DFE C 2471 G 2479 CGUCCACAG > HL_32735.2 7A0S A 2450 U 2458 AGUCCAUAU > HL_32735.2 8CRE C 2812 G 2820 CGUUCAUAG > HL_32735.2 4V9F A 2506 U 2514 AGCACAUAU