| 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 5 2 | 5 5 I | 6 6 3 | 7 6 I | 8 6 4 | 9 6 I | 10 6 5 | 11 6 I | 12 6 6 | 13 6 I | 14 6 7 | 15 5 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_89881.5_Instance_1 HL_89881.5,HL_4LFB_001,U12_G22 | U | U | U | G | A | U | C | C | U | G | G | |||||||||||||||
| HL_89881.5_Sequence_1 HL_89881.54LFB_U12_G22 | U | U | U | G | A | U | C | C | U | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_89881.5_Instance_2 HL_89881.5,HL_5J7L_001,U12_G22 | U | U | U | G | A | U | C | A | U | G | G | |||||||||||||||
| HL_89881.5_Sequence_2 HL_89881.55J7L_U12_G22 | U | U | U | G | A | U | C | A | U | G | G | true | 96 | 0 | 0 | 0.85 | ||||||||||
| HL_89881.5_Instance_3 HL_89881.5,HL_8CRE_191,G7_C17 | G | U | U | G | A | U | C | C | U | G | C | |||||||||||||||
| HL_89881.5_Sequence_3 HL_89881.58CRE_G7_C17 | G | U | U | G | A | U | C | C | U | G | C | true | 98 | 0 | 0 | 0.32 | ||||||||||
| HL_89881.5_Instance_4 HL_89881.5,HL_8P9A_190,G7_C17 | G | U | U | G | A | U | C | C | U | G | C | |||||||||||||||
| HL_89881.5_Sequence_4 HL_89881.58P9A_G7_C17 | G | U | U | G | A | U | C | C | U | G | C | true | 98 | 0 | 0 | 0.32 |
1 10 cWW 2 8 tHW 2 9 s55 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35 8 9 s35 9 10 s35JAR3D SCFG/MRF model for HL_89881.5:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.010288190,0.016798501,0.012436975,0.117003488,0.000000000],[0.156744404,0.018387268,0.120330946,0.014377162,0.000000000],[0.012529891,0.139891527,0.002645835,0.020320157,0.000000000],[0.139728745,0.013959612,0.192864020,0.011693279,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U12 - G22 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right for 4LFB|1|A|U|20 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | 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 BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.018693135,0.331785735,0.003836508,0.037788963,0.000000000],[0.003836508,0.044769116,0.012004616,0.003836508,0.000000000],[0.033285442,0.003836508,0.024671698,0.015679068,0.000000000],[0.003836508,0.003836508,0.036190878,0.422112303,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.083333333,0.083333333,0.083333333,0.750000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair U13 - U20 tHW HairpinNode | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G15:C19 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.750000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 Interaction | Interacting Bases [2,2] | Pair Probability [[0.750000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A16 Interaction | Interacting Bases [3,3] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17 Interaction | Interacting Bases [4,4] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C18 Interaction | Interacting Bases [5,5] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.583333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.083333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.083333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C19Sequences of instances from HL_89881.5:
> HL_89881.5 4LFB U 12 G 22 UUUGAUCCUGG > HL_89881.5 5J7L U 12 G 22 UUUGAUCAUGG > HL_89881.5 8CRE G 7 C 17 GUUGAUCCUGC > HL_89881.5 8P9A G 7 C 17 GUUGAUCCUGC