| 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 4 4 | 9 4 I | 10 4 5 | 11 5 I | 12 6 6 | 13 7 I | 14 8 7 | 15 8 I | 16 9 | 17 8 I | 18 8 8 | 19 5 I | 20 4 9 | 21 4 I | 22 4 10 | 23 4 I | 24 4 11 | 25 4 I | 26 4 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_50521.1_Instance_1 IL_50521.1_IL_1FJG_017_G409_C433 | G | G | A | A | G | A | A | G | U | G | U | A | A | A | C | |||||||||||||||||||||
| IL_50521.1_Sequence_1 IL_50521.1_IL_1FJG_017_G409_C433 | G | G | A | A | G | A | A | G | * | U | G | U | A | A | A | C | true | 98 | 0 | 0 | 0.37 | |||||||||||||||
| IL_50521.1_Instance_2 IL_50521.1_IL_2AW7_020_U409_G433 | U | G | A | A | G | A | A | G | U | G | U | A | A | A | G | |||||||||||||||||||||
| IL_50521.1_Sequence_2 IL_50521.1_IL_2AW7_020_U409_G433 | U | G | A | A | G | A | A | G | * | U | G | U | A | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 14 cWW 2 10 s33 2 13 tSH 3 4 s35 3 9 s35 3 10 s55 3 11 tWH 4 9 tSS 5 6 s35 5 11 tHW 5 12 s55 6 7 s35 7 8 cWW 8 9 s33 9 11 s55 10 12 cWH 11 12 s35 12 13 s35 13 14 s35 9 5 6BPh 2 12 6BPh 13 2 6BRJAR3D SCFG/MRF model for IL_50521.1:
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 [14] // Initial node G409 - C433 from junction BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.011606602,0.017778352,0.013679584,0.116107298,0.000000000],[0.167090224,0.012234263,0.126818052,0.015364421,0.000000000],[0.013781309,0.136797428,0.002838808,0.021529953,0.000000000],[0.118996443,0.014843715,0.198100860,0.012432686,0.000000000],[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 [14] // Basepair G409 - C433 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.043716223,0.050956855,0.000526725,0.002508196,0.000000000],[0.044105167,0.046228647,0.000526725,0.000526725,0.000000000],[0.388315159,0.003687073,0.017863095,0.306690455,0.000000000],[0.047517987,0.045777520,0.000526725,0.000526725,0.000000000],[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 [2] | Right Index [13] // Basepair G410 - A432 tSH ClusterNode | Deletion Probability [0.000000000000000000385733987058166880000000000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [3] | Right Index [12] | Norm Constant [0.409673001779593] // Cluster node A411:A414 and G428:A431 Interaction | Interacting Bases [2,4] | Pair Probability [[0.004207186,0.005280481,0.062750142,0.005167681,0.000000000],[0.000917983,0.000917983,0.006425879,0.000917983,0.000000000],[0.082535231,0.085064800,0.662195716,0.074439110,0.000000000],[0.000917983,0.000917983,0.006425879,0.000917983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G413 - G428 tSS Interaction | Interacting Bases [1,6] | Pair Probability [[0.418144609,0.003985368,0.341751342,0.003985368,0.000000000],[0.031463906,0.014640658,0.022813077,0.003985368,0.000000000],[0.003985368,0.003985368,0.049366656,0.035560217,0.000000000],[0.019002964,0.003985368,0.023593614,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A411 - A430 tWH Interaction | Interacting Bases [3,6] | Pair Probability [[0.418144609,0.031463906,0.003985368,0.019002964,0.000000000],[0.003985368,0.014640658,0.003985368,0.003985368,0.000000000],[0.341751342,0.022813077,0.049366656,0.023593614,0.000000000],[0.003985368,0.003985368,0.035560217,0.019750751,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A414 - A430 tHW Interaction | Interacting Bases [5,7] | Pair Probability [[0.003460772,0.003460772,0.017164318,0.012348510,0.000000000],[0.003460772,0.037017516,0.016981393,0.188883971,0.000000000],[0.015181754,0.003460772,0.013849500,0.003460772,0.000000000],[0.365685069,0.003460772,0.277303821,0.034819514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U429 - A431 cWH Insertion | Location [1] | Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000]// Insertion after nucleotide 3, position 1 in cluster node InitialNode | 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 [6] | Right Index [8] // Initial node A415 - U427 from junction FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [6] | Right Index [8] // Fixed node on left InitialNode | 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 [1.000000000] | 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 [[0.016500430,0.310288742,0.015571103,0.044672112,0.000000000],[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]] | 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 G416 - U427 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_50521.1:
> IL_50521.1 IL_1FJG_017 G 409 C 433 GGAAGAAG*UGUAAAC > IL_50521.1 IL_2AW7_020 U 409 G 433 UGAAGAAG*UGUAAAG