| 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 6 I | 6 7 | 7 6 I | 8 5 3 | 9 5 I | 10 5 4 | 11 5 I | 12 5 5 | 13 5 I | 14 5 6 | 15 5 I | 16 5 7 | 17 5 I | 18 5 8 | 19 4 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_82563.1_Instance_1 IL_82563.1_IL_2GDI_006_U20_A45 | U | G | C | U | G | A | G | A | A | A | ||||||||||||||||||
| IL_82563.1_Sequence_1 IL_82563.1_IL_2GDI_006_U20_A45 | U | G | * | C | U | G | A | G | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_82563.1_Instance_2 IL_82563.1_IL_2GDI_002_U20_A45 | U | G | C | U | G | A | G | A | A | A | ||||||||||||||||||
| IL_82563.1_Sequence_2 IL_82563.1_IL_2GDI_002_U20_A45 | U | G | * | C | U | G | A | G | A | A | A | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_82563.1_Instance_3 IL_82563.1_IL_2HOJ_002_U20_A45 | U | G | C | U | G | A | G | A | A | A | ||||||||||||||||||
| IL_82563.1_Sequence_3 IL_82563.1_IL_2HOJ_002_U20_A45 | U | G | * | C | U | G | A | G | A | A | A | true | 100 | 0 | 0 | 0.00 |
1 9 s35 1 10 cWW 2 3 cWW 2 4 s55 2 8 s53 3 4 s35 4 5 s35 4 8 tWH 5 7 s33 5 8 s55 6 7 s35 9 10 s55 5 8 6BPhJAR3D SCFG/MRF model for IL_82563.1:
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 [10] // Initial node U20 - A45 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009027553,0.019940410,0.009723686,0.205285714,0.000000000],[0.024262390,0.009440542,0.191977271,0.010276342,0.000000000],[0.009740283,0.190868689,0.002132868,0.023419534,0.000000000],[0.242412981,0.010204177,0.027588121,0.013699440,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair U20 - A45 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | 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 [0.993970181,0.005999820,0.000029999] | 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 ClusterNode | Deletion Probability [0.000000000000000078125000000000012000000000000000000000000000] | Num Left Bases [1] | Num Right Bases [6] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node G21:G21 and C38:A43 Interaction | Interacting Bases [1,2] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - C38 cWW Interaction | Interacting Bases [3,7] | Pair Probability [[0.025719646,0.005394014,0.026458819,0.005394014,0.000000000],[0.053578574,0.044783309,0.035804622,0.005394014,0.000000000],[0.005394014,0.005394014,0.063126898,0.025161497,0.000000000],[0.568527570,0.005394014,0.066543467,0.057931515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U39 - A43 tWH Interaction | Interacting Bases [4,4] | Pair Probability [[0.021739130,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.021739130,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.934782609,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.021739130,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G40 Interaction | Interacting Bases [5,5] | Pair Probability [[0.700000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A41 Interaction | Interacting Bases [6,6] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.700000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion G42 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 [3] | Right Index [2] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | 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_82563.1:
> IL_82563.1 IL_2GDI_006 U 20 A 45 UG*CUGAGAAA > IL_82563.1 IL_2GDI_002 U 20 A 45 UG*CUGAGAAA > IL_82563.1 IL_2HOJ_002 U 20 A 45 UG*CUGAGAAA