| 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 4 I | 6 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 9 5 | 11 10 I | 12 15 6 | 13 15 I | 14 16 | 15 15 I | 16 15 7 | 17 14 I | 18 13 8 | 19 12 I | 20 11 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_69145.3_Instance_1 IL_69145.3,IL_5FJC_004,U64_A85 | U | C | C | U | G | C | G | A | A | A | ||||||||||||||||||
| IL_69145.3_Sequence_1 IL_69145.35FJC_U64_A85 | U | C | C | U | G | C | * | G | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_69145.3_Instance_2 IL_69145.3,IL_4AOB_004,U64_A85 | U | C | C | U | G | C | G | A | A | A | ||||||||||||||||||
| IL_69145.3_Sequence_2 IL_69145.34AOB_U64_A85 | U | C | C | U | G | C | * | G | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_69145.3_Instance_3 IL_69145.3,IL_4KQY_006,U85_A109 | U | C | C | A | G | C | G | G | A | A | ||||||||||||||||||
| IL_69145.3_Sequence_3 IL_69145.34KQY_U85_A109 | U | C | C | A | G | C | * | G | G | A | A | true | 91 | 0 | 0 | 1.69 | ||||||||||||
| IL_69145.3_Instance_4 IL_69145.3,IL_3V7E_005,U96_A117 | U | C | C | U | G | C | G | A | A | A | ||||||||||||||||||
| IL_69145.3_Sequence_4 IL_69145.33V7E_U96_A117 | U | C | C | U | G | C | * | G | A | A | A | true | 100 | 0 | 0 | 0.00 |
1 10 cWW 2 3 s35 3 4 s35 4 5 s35 5 6 perp 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 9 10 s35 6 5 7BPhJAR3D SCFG/MRF model for IL_69145.3:
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 [[0.008860598,0.017207362,0.009719508,0.192545756,0.000000000],[0.021620030,0.009642604,0.193193575,0.010832498,0.000000000],[0.009738465,0.190721067,0.002004937,0.022604323,0.000000000],[0.238955281,0.010175052,0.052269656,0.009909289,0.000000000],[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 U64 - A85 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 5FJC|1|A|C|65 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 5FJC|1|A|C|66 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.083333333,0.583333333,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left for 5FJC|1|A|U|67 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [9] // Fixed node on left for 5FJC|1|A|G|68 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [6] | Right Index [9] // Fixed node on right for 5FJC|1|A|A|84 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 [6] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [2] | Left Index [6] | Right Index [8] // Fixed node on right for 5FJC|1|A|A|83 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 [6] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003672434,0.006585557,0.004221915,0.076551649,0.000000000],[0.054657564,0.026181875,0.601780983,0.037174395,0.000000000],[0.004269328,0.078201131,0.000804742,0.009036584,0.000000000],[0.077544064,0.005116688,0.010309321,0.003891769,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [6] | Right Index [7] // Basepair C69 - G82 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node type * Interaction | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncationSequences of instances from IL_69145.3:
> IL_69145.3 5FJC U 64 A 85 UCCUGC*GAAA > IL_69145.3 4AOB U 64 A 85 UCCUGC*GAAA > IL_69145.3 4KQY U 85 A 109 UCCAGC*GGAA > IL_69145.3 3V7E U 96 A 117 UCCUGC*GAAA