| 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 5 I | 8 6 4 | 9 7 I | 10 8 5 | 11 9 I | 12 10 6 | 13 11 I | 14 20 7 | 15 20 I | 16 21 | 17 20 I | 18 20 8 | 19 19 I | 20 18 9 | 21 17 I | 22 16 10 | 23 15 I | 24 14 11 | 25 13 I | 26 12 12 | 27 3 I | 28 3 13 | 29 2 I | 30 2 14 | 31 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_82188.2_Instance_1 IL_82188.2_IL_4A1B_090_U2206_G2229 | U | C | A | A | A | G | U | A | A | C | C | A | A | G | ||||||||||||||||||||||
| IL_82188.2_Sequence_1 IL_82188.2_IL_4A1B_090_U_2206_G_2229 | U | C | A | A | A | G | U | * | A | A | C | C | A | A | G | true | 99 | 0 | 0 | 0.10 | ||||||||||||||||
| IL_82188.2_Instance_2 IL_82188.2_IL_1S72_069_U1907_G1932 | U | G | A | A | C | A | C | G | A | C | G | A | A | G | ||||||||||||||||||||||
| IL_82188.2_Sequence_2 IL_82188.2_IL_1S72_069_U_1907_G_1932 | U | G | A | A | C | A | C | * | G | A | C | G | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_82188.2_Instance_3 IL_82188.2_IL_2QBZ_005_A60_U81 | A | A | A | A | A | U | G | C | G | C | C | A | A | U | ||||||||||||||||||||||
| IL_82188.2_Sequence_3 IL_82188.2_IL_2QBZ_005_A60_U81 | A | A | A | A | A | U | G | * | C | G | C | C | A | A | U | true | 94 | 0 | 0 | 0.99 | ||||||||||||||||
| IL_82188.2_Instance_4 IL_82188.2_IL_2OIU_002_C21_G40 | C | G | A | C | C | A | G | C | U | C | U | U | A | G | ||||||||||||||||||||||
| IL_82188.2_Sequence_4 IL_82188.2_IL_2OIU_002_C21_G40 | C | G | A | C | C | A | G | * | C | U | C | U | U | A | G | true | 85 | 0 | 0 | 2.60 |
1 2 s35 1 14 cWW 2 11 s33 2 13 tSH 3 4 s35 3 12 s55 4 5 s35 5 6 s35 6 7 s35 7 8 cWW 7 9 s55 8 9 s35 9 10 s35 10 11 s35 12 13 s35 13 14 s35 13 2 6BRJAR3D SCFG/MRF model for IL_82188.2:
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 [14] // Initial node U2206 - G2229 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011111603,0.017461516,0.012891603,0.128456516,0.000000000],[0.165459031,0.012258289,0.131655760,0.014499055,0.000000000],[0.013096582,0.117654275,0.002783975,0.020240771,0.000000000],[0.120520778,0.013521174,0.204788661,0.013600411,0.000000000],[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 [14] // Basepair U2206 - G2229 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.139603202,0.125397335,0.001423599,0.008606663,0.000000000],[0.140035475,0.099564092,0.001423599,0.001423599,0.000000000],[0.148901219,0.001423599,0.009176075,0.064154364,0.000000000],[0.130375178,0.125644805,0.001423599,0.001423599,0.000000000],[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 [2] | Right Index [13] // Basepair C2207 - A2228 tSH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [3] | Right Index [12] // Fixed node on left 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.250000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [4] | Right Index [12] // Fixed node on left 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.416666667,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [5] | Right Index [12] // Fixed node on left 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 [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Position [1] | Left Index [6] | Right Index [12] // Fixed node on left 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 [7] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.083333333,0.250000000,0.000000000] | Position [2] | Left Index [7] | Right Index [12] // Fixed node on right 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 [7] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.250000000,0.250000000,0.000000000] | Position [2] | Left Index [7] | Right Index [11] // Fixed node on right 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 [7] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [7] | Right Index [10] // Fixed node on right 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 [7] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.250000000,0.250000000,0.000000000] | Position [2] | Left Index [7] | Right Index [9] // Fixed node on right 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 [7] | Right Index [8] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009694180,0.019340841,0.011054737,0.192879225,0.000000000],[0.019536413,0.008560570,0.212050526,0.012463012,0.000000000],[0.011022420,0.223001642,0.002109324,0.025151587,0.000000000],[0.204201759,0.012606770,0.025255099,0.011071894,0.000000000],[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 [7] | Right Index [8] // Basepair U2212 - A2223 cWW HairpinNode | Num Bases [1] | Left Index [8] | Right Index [8] | 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_82188.2:
> IL_82188.2 IL_4A1B_090 U 2206 G 2229 UCAAAGU*AACCAAG > IL_82188.2 IL_1S72_069 U 1907 G 1932 UGAACAC*GACGAAG > IL_82188.2 IL_2QBZ_005 A 60 U 81 AAAAAUG*CGCCAAU > IL_82188.2 IL_2OIU_002 C 21 G 40 CGACCAG*CUCUUAG