| 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_36421.4_Instance_1 HL_36421.4_HL_5J7L_193_A2471_U2479 | A | G | U | U | C | A | U | A | U | |||||||||||||||
| HL_36421.4_Sequence_1 HL_36421.4_HL_5J7L_193_A_2471_U_2479 | A | G | U | U | C | A | U | A | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_36421.4_Instance_2 HL_36421.4_HL_4Y4O_163_C2471_G2479 | C | G | U | C | C | A | C | A | G | |||||||||||||||
| HL_36421.4_Sequence_2 HL_36421.4_HL_4Y4O_163_C_2471_G_2479 | C | G | U | C | C | A | C | A | G | true | 88 | 0 | 0 | 1.96 | ||||||||||
| HL_36421.4_Instance_3 HL_36421.4_HL_4WF9_056_A2498_U2506 | A | G | U | U | C | A | C | A | U | |||||||||||||||
| HL_36421.4_Sequence_3 HL_36421.4_HL_4WF9_056_A_2498_U_2506 | A | G | U | U | C | A | C | A | U | true | 97 | 0 | 0 | 0.59 | ||||||||||
| HL_36421.4_Instance_4 HL_36421.4_HL_7A0S_059_A2450_U2458 | A | G | U | C | C | A | U | A | U | |||||||||||||||
| HL_36421.4_Sequence_4 HL_36421.4_HL_7A0S_059_A_2450_U_2458 | A | G | U | C | C | A | U | A | U | true | 98 | 0 | 0 | 0.39 | ||||||||||
| HL_36421.4_Instance_5 HL_36421.4_HL_4V9F_062_A2506_U2514 | A | G | C | A | C | A | U | A | U | |||||||||||||||
| HL_36421.4_Sequence_5 HL_36421.4_HL_4V9F_062_A_2506_U_2514 | A | G | C | A | C | A | U | A | U | true | 86 | 0 | 0 | 2.35 | ||||||||||
| HL_36421.4_Instance_6 HL_36421.4_HL_5TBW_061_C2840_G2848 | C | G | U | U | C | A | U | A | G | |||||||||||||||
| HL_36421.4_Sequence_6 HL_36421.4_HL_5TBW_061_C_2840_G_2848 | C | G | U | U | C | A | U | A | G | true | 94 | 0 | 0 | 0.98 |
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 9 8 7BPh 8 2 6BR 1 6 7BRJAR3D SCFG/MRF model for HL_36421.4:
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 [9] // Initial node A2471 - U2479 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004620414,0.010085180,0.005057588,0.548501215,0.000000000],[0.018014501,0.008765314,0.206090237,0.019188450,0.000000000],[0.002883321,0.054580502,0.000563633,0.046343014,0.000000000],[0.054235572,0.003360490,0.006861583,0.010848985,0.000000000],[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 [[0.042049014,0.044514549,0.000504770,0.002378984,0.000000000],[0.042361408,0.044411471,0.000504770,0.000504770,0.000000000],[0.409943044,0.003533393,0.017273635,0.299901013,0.000000000],[0.046937930,0.044171708,0.000504770,0.000504770,0.000000000],[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 [0.999999999999999] // Hairpin node U2473:U2477 Interaction | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.687500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2473 Interaction | Interacting Bases [2,2] | Pair Probability [[0.170454545,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.329545455,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.011363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.488636364,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2474 Interaction | Interacting Bases [3,3] | Pair Probability [[0.001689189,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.994932432,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.001689189,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.001689189,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2475 Interaction | Interacting Bases [4,4] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2476 Interaction | Interacting Bases [5,5] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U2477Sequences of instances from HL_36421.4:
> HL_36421.4 HL_5J7L_193 A 2471 U 2479 AGUUCAUAU > HL_36421.4 HL_4Y4O_163 C 2471 G 2479 CGUCCACAG > HL_36421.4 HL_4WF9_056 A 2498 U 2506 AGUUCACAU > HL_36421.4 HL_7A0S_059 A 2450 U 2458 AGUCCAUAU > HL_36421.4 HL_4V9F_062 A 2506 U 2514 AGCACAUAU > HL_36421.4 HL_5TBW_061 C 2840 G 2848 CGUUCAUAG