| 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 | 7 4 I | 8 3 3 | 9 3 I | 10 3 4 | 11 2 I | 12 2 5 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_67887.1_Instance_1 IL_67887.1_IL_3RW6_003_A20_U41 | A | G | U | A | A | U | ||||||||||||
| IL_67887.1_Sequence_1 IL_67887.1_IL_3RW6_003_A20_U41 | A | G | * | U | A | A | U | true | 94 | 0 | 0 | 0.54 | ||||||
| IL_67887.1_Instance_2 IL_67887.1_IL_4FAW_005_G128_U238 | G | G | U | U | G | A | U | |||||||||||
| IL_67887.1_Sequence_2 IL_67887.1_IL_4FAW_005_G128_U238 | G | G | * | U | U | G | A | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 5 cWW 2 3 cWW 2 4 tSH 2 5 s55 3 5 s35 4 5 s35JAR3D SCFG/MRF model for IL_67887.1:
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 [5] // Initial node A20 - U41 from junction BasepairNode | Deletion Probability [0.0000015195492620] | Pair Probability [[0.012875655,0.167362170,0.012690460,0.139544678,0.000000000],[0.017278970,0.010426425,0.115221913,0.012854497,0.000000000],[0.012509796,0.118823330,0.002800872,0.196378937,0.000000000],[0.122336675,0.013723253,0.019374350,0.025798019,0.000000000],[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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair A20 - U41 cWW ClusterNode | Deletion Probability [0.0000000006171744] | Num Left Bases [1] | Num Right Bases [2] | Left Index [2] | Right Index [4] | Norm Constant [0.316951872077325] // Cluster node G21:G21 and U38:A40 Interaction | Interacting Bases [1,2] | Pair Probability [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[0.014475176,0.011549597,0.038212544,0.015431970,0.000000000],[0.015226490,0.044298882,0.003453650,0.364972803,0.000000000],[0.037922120,0.017096803,0.015161977,0.035165601,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - U38 cWW Interaction | Interacting Bases [1,3] | Pair Probability [[0.073244666,0.074626455,0.002664993,0.188942478,0.000000000],[0.070262839,0.067908836,0.002664993,0.002664993,0.000000000],[0.086862504,0.002664993,0.212156020,0.069245779,0.000000000],[0.072228285,0.068532177,0.002664993,0.002664993,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G21 - A40 tSH Insertion | Location [2] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node 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_67887.1:
> IL_67887.1 IL_3RW6_003 A 20 U 41 AG*UAAU > IL_67887.1 IL_4FAW_005 G 128 U 238 GG*UUGAU