| 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 5 4 | 9 6 I | 10 7 5 | 11 8 I | 12 9 6 | 13 9 I | 14 10 | 15 9 I | 16 9 7 | 17 4 I | 18 4 8 | 19 3 I | 20 3 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_21200.1_Instance_1 IL_21200.1,IL_6DLR_001,C45_G15 | C | A | A | G | U | G | C | U | A | G | ||||||||||||||||||
| IL_21200.1_Sequence_1 IL_21200.16DLR_C45_G15 | C | A | A | G | U | G | * | C | U | A | G | true | 94 | 0 | 0 | 0.85 | ||||||||||||
| IL_21200.1_Instance_2 IL_21200.1,IL_6CK5_001,C45_G15 | C | G | A | G | C | G | C | U | A | G | ||||||||||||||||||
| IL_21200.1_Sequence_2 IL_21200.16CK5_C45_G15 | C | G | A | G | C | G | * | C | U | A | G | true | 98 | 0 | 0 | 0.36 | ||||||||||||
| IL_21200.1_Instance_3 IL_21200.1,IL_5T83_001,C42_G15 | C | A | A | G | A | G | C | U | A | G | ||||||||||||||||||
| IL_21200.1_Sequence_3 IL_21200.15T83_C42_G15 | C | A | A | G | A | G | * | C | U | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_21200.1_Instance_4 IL_21200.1,IL_6DME_001,C40_G14 | C | A | A | G | C | G | C | U | A | G | ||||||||||||||||||
| IL_21200.1_Sequence_4 IL_21200.16DME_C40_G14 | C | A | A | G | C | G | * | C | U | A | G | true | 98 | 0 | 0 | 0.34 | ||||||||||||
| IL_21200.1_Instance_5 IL_21200.1,IL_7MLW_002,C51_G10 | C | G | A | G | A | G | C | U | A | G | ||||||||||||||||||
| IL_21200.1_Sequence_5 IL_21200.17MLW_C51_G10 | C | G | A | G | A | G | * | C | U | A | G | true | 100 | 0 | 0 | 0.02 | ||||||||||||
| IL_21200.1_Instance_6 IL_21200.1,IL_5U3G_001,C30_G9 | C | G | A | G | A | G | C | U | A | G | ||||||||||||||||||
| IL_21200.1_Sequence_6 IL_21200.15U3G_C30_G9 | C | G | A | G | A | G | * | C | U | A | G | true | 100 | 0 | 0 | 0.02 |
1 2 s35 1 10 cWW 2 8 s33 2 9 tSH 2 10 s55 3 6 s35 3 8 tHW 3 9 s55 4 5 s35 6 7 cWW 6 8 s55 7 8 s35 8 9 s35 9 10 s35 9 2 6BRJAR3D SCFG/MRF model for IL_21200.1:
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 [0.0000244705618206] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [10] // Basepair C45 - G15 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.167665565,0.067359863,0.001502363,0.008259478,0.000000000],[0.137181713,0.091101634,0.001502363,0.001502363,0.000000000],[0.164326245,0.001502363,0.010577419,0.073847469,0.000000000],[0.137198290,0.133468145,0.001502363,0.001502363,0.000000000],[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 [9] // Basepair A46 - A14 tSH BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.017712837,0.039419550,0.003919879,0.467089651,0.000000000],[0.003919879,0.315867349,0.009396209,0.003919879,0.000000000],[0.018397680,0.003919879,0.029810350,0.022742669,0.000000000],[0.003919879,0.003919879,0.017434273,0.038610158,0.000000000],[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 [3] | Right Index [8] // Basepair A47 - U13 tHW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 6DLR|1|A|G|15 InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.437500000,0.312500000,0.062500000,0.187500000,0.000000000] | Position [1] | Left Index [5] | Right Index [7] // Fixed node on left for 6DLR|1|A|C|45 InitialNode | 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 [1.000000000] | 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 [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[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 G50 - C12 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_21200.1:
> IL_21200.1 6DLR C 45 G 15 CAAGUG*CUAG > IL_21200.1 6CK5 C 45 G 15 CGAGCG*CUAG > IL_21200.1 5T83 C 42 G 15 CAAGAG*CUAG > IL_21200.1 6DME C 40 G 14 CAAGCG*CUAG > IL_21200.1 7MLW C 51 G 10 CGAGAG*CUAG > IL_21200.1 5U3G C 30 G 9 CGAGAG*CUAG