| 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 3 | 7 5 I | 8 5 4 | 9 5 I | 10 5 5 | 11 5 I | 12 5 6 | 13 5 I | 14 5 7 | 15 5 I | 16 5 8 | 17 5 I | 18 5 9 | 19 6 I | 20 7 10 | 21 7 I | 22 8 | 23 7 I | 24 7 11 | 25 6 I | 26 5 12 | 27 2 I | 28 2 13 | 29 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_89028.6_Instance_1 IL_89028.6_IL_3V2F_074_C1934_G1964 | C | G | A | A | A | U | U | C | C | U | U | G | C | C | U | G | ||||||||||||||||||
| IL_89028.6_Sequence_1 IL_89028.6_IL_3V2F_074_C_1934_G_1964 | C | G | A | A | A | U | U | C | C | U | U | G | * | C | C | U | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_89028.6_Instance_2 IL_89028.6_IL_4A1B_092_C2272_G2302 | C | C | A | A | A | U | G | C | C | U | C | G | C | G | C | G | ||||||||||||||||||
| IL_89028.6_Sequence_2 IL_89028.6_IL_4A1B_092_C_2272_G_2302 | C | C | A | A | A | U | G | C | C | U | C | G | * | C | G | C | G | true | 93 | 0 | 0 | 1.52 | ||||||||||||
| IL_89028.6_Instance_3 IL_89028.6_IL_2QBG_077_C1934_G1964 | C | G | A | A | A | U | U | C | C | U | U | G | C | C | U | G | ||||||||||||||||||
| IL_89028.6_Sequence_3 IL_89028.6_IL_2QBG_077_C_1934_G_1964 | C | G | A | A | A | U | U | C | C | U | U | G | * | C | C | U | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 13 cWW 2 12 s33 2 13 s55 3 6 s33 3 9 cHW 3 10 s55 3 12 tSS 4 5 s33 4 6 perp 6 8 cSH 7 8 s35 8 9 s33 10 11 cWW 11 12 s35 11 3 7BPh 12 3 6BPh 2 13 6BPh 7 6 7BR 2 12 6BR 2 13 2BRJAR3D SCFG/MRF model for IL_89028.6:
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 [13] // Initial node C1934 - G1964 from junction BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.009933419,0.017038443,0.011544982,0.190528657,0.000000000],[0.020571967,0.008484264,0.242033011,0.013790371,0.000000000],[0.011692161,0.206400787,0.002129068,0.023556849,0.000000000],[0.191635263,0.013137326,0.027308888,0.010214543,0.000000000],[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 [0.016116035,0.966962127,0.016116035,0.000805802] | Right Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Left Index [1] | Right Index [13] // Basepair C1934 - G1964 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.004672897,0.331775701,0.658878505,0.004672897,0.000000000] | Position [1] | Left Index [2] | Right Index [12] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [12] // New Initial node after Fixed node ClusterNode | Deletion Probability [0.000000000000000000001936518681344305600000000000000000000000] | Num Left Bases [7] | Num Right Bases [1] | Left Index [3] | Right Index [12] | Norm Constant [0.407484593358929] // Cluster node A1936:U1943 and C1962:C1962 Interaction | Interacting Bases [1,8] | Pair Probability [[0.073067940,0.412022438,0.334763565,0.074730107,0.000000000],[0.000848435,0.003498818,0.003288659,0.000848435,0.000000000],[0.004287379,0.017403729,0.030341845,0.036414305,0.000000000],[0.000848435,0.003498818,0.003288659,0.000848435,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1936 - C1962 tSS Interaction | Interacting Bases [4,6] | Pair Probability [[0.059404396,0.065785017,0.016428777,0.012214180,0.000000000],[0.059861207,0.055485992,0.002480374,0.058302387,0.000000000],[0.009643499,0.202599412,0.020015679,0.057773311,0.000000000],[0.185904450,0.136229460,0.002480374,0.055391485,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1940 - C1942 cSH Interaction | Interacting Bases [1,7] | Pair Probability [[0.003263974,0.003263974,0.014318437,0.401755682,0.000000000],[0.003263974,0.034912497,0.003263974,0.003263974,0.000000000],[0.016188261,0.016015738,0.013061942,0.261534810,0.000000000],[0.011646306,0.178142997,0.003263974,0.032839487,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1936 - U1943 cHW Interaction | Interacting Bases [2,2] | 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]] // Left strand conserved insertion A1937 Interaction | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion U1939 Interaction | Interacting Bases [5,5] | Pair Probability [[0.029411765,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.911764706,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion C1941 Insertion | Location [2] | Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000]// Insertion after nucleotide 4, position 2 in cluster node InitialNode | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [11] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.003914340,0.055820081,0.004532224,0.074283445,0.000000000],[0.006604600,0.022593563,0.080006995,0.005092413,0.000000000],[0.004475173,0.606828618,0.000825289,0.010585725,0.000000000],[0.073854492,0.037418864,0.009131325,0.004032852,0.000000000],[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 [10] | Right Index [11] // Basepair G1945 - C1961 cWW HairpinNode | Num Bases [1] | Left Index [11] | Right Index [11] | 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_89028.6:
> IL_89028.6 IL_3V2F_074 C 1934 G 1964 CGAAAUUCCUUG*CCUG > IL_89028.6 IL_4A1B_092 C 2272 G 2302 CCAAAUGCCUCG*CGCG > IL_89028.6 IL_2QBG_077 C 1934 G 1964 CGAAAUUCCUUG*CCUG