| 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 5 3 | 7 5 I | 8 5 4 | 9 5 I | 10 5 5 | 11 6 I | 12 7 | 13 6 I | 14 5 6 | 15 4 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_39355.1_Instance_1 IL_39355.1_IL_4A1B_119_U3036_A3083 | U | A | A | U | U | A | C | C | A | |||||||||||||||
| IL_39355.1_Sequence_1 IL_39355.1_IL_4A1B_119_U_3036_A_3083 | U | A | A | U | U | * | A | C | C | A | true | 100 | 0 | 0 | 0.00 | |||||||||
| IL_39355.1_Instance_2 IL_39355.1_IL_3U5H_123_U3047_A3094 | U | A | A | U | U | A | C | C | A | |||||||||||||||
| IL_39355.1_Sequence_2 IL_39355.1_IL_3U5H_123_U_3047_A_3094 | U | A | A | U | U | * | A | C | C | A | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 8 cWW 2 6 tHH 2 8 s35 3 4 s35 4 5 s35 5 6 cWW 6 7 perp 6 8 s35 2 6 6BPh 4 8 6BRJAR3D SCFG/MRF model for IL_39355.1:
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 [8] // Initial node U3036 - A3083 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair U3036 - A3083 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [2] | Right Index [7] // 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 [0.023781213,0.951248514,0.023781213,0.001189061] | Right Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Left Index [2] | Right Index [6] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [6] | Norm Constant [0.262851887903713] // Cluster node A3037:U3040 and A3080:A3080 Interaction | Interacting Bases [1,5] | Pair Probability [[0.602055362,0.099581892,0.024626999,0.024664424,0.000000000],[0.009101432,0.000704744,0.060585658,0.050059363,0.000000000],[0.004402684,0.058476991,0.001726538,0.000704744,0.000000000],[0.004330659,0.057569022,0.000704744,0.000704744,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A3037 - A3080 tHH Interaction | Interacting Bases [4,5] | Pair Probability [[0.009116058,0.020135905,0.009819016,0.207298319,0.000000000],[0.024500257,0.009533097,0.193859401,0.010377090,0.000000000],[0.009835776,0.192739951,0.002153778,0.023649137,0.000000000],[0.234985657,0.010304218,0.027858593,0.013833748,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U3040 - A3080 cWW Interaction | Interacting Bases [2,2] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A3038 Interaction | Interacting Bases [3,3] | Pair Probability [[0.041666667,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.875000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U3039 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 [6] | Right Index [5] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_39355.1:
> IL_39355.1 IL_4A1B_119 U 3036 A 3083 UAAUU*ACCA > IL_39355.1 IL_3U5H_123 U 3047 A 3094 UAAUU*ACCA