| 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 3 3 | 7 4 I | 8 5 4 | 9 6 I | 10 7 5 | 11 8 I | 12 13 6 | 13 13 I | 14 14 7 | 15 14 I | 16 15 | 17 14 I | 18 14 8 | 19 13 I | 20 13 9 | 21 12 I | 22 11 10 | 23 10 I | 24 9 11 | 25 4 I | 26 3 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_52940.1_Instance_1 IL_52940.1_IL_1FJG_049_U1247_G1290 | U | A | C | A | A | A | G | C | A | A | A | A | A | G | ||||||||||||||||||||||
| IL_52940.1_Sequence_1 IL_52940.1_IL_1FJG_049_U_1247_G_1290 | U | A | C | A | A | A | G | * | C | A | A | A | A | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||||||
| IL_52940.1_Instance_2 IL_52940.1_IL_3U5F_076_G1480_C1527 | G | C | C | A | G | C | G | A | U | U | G | U | G | A | A | A | C | |||||||||||||||||||
| IL_52940.1_Sequence_2 IL_52940.1_IL_3U5F_076_G_1480_C_1527 | G | C | C | A | G | C | G | A | * | U | U | G | U | G | A | A | A | C | true | 79 | 0 | 0 | 3.54 |
1 14 cWW 2 3 s35 2 12 tWH 2 13 tWH 2 14 s55 3 4 s35 3 11 s55 3 12 tWH 4 5 s35 4 11 s55 5 6 s35 6 7 s35 6 9 tWW 7 8 cWW 8 9 s33 9 10 s55 11 12 s35 12 13 s35 13 14 s35JAR3D SCFG/MRF model for IL_52940.1:
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 U1247 - G1290 from junction BasepairNode | Deletion Probability [0.0000015195492620] | 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 [0.493381468,0.493381468,0.012635379,0.000601685] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | 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 U1247 - G1290 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [2] | Num Right Bases [2] | Left Index [2] | Right Index [13] | Norm Constant [0.096189158088804] // Cluster node A1248:C1249 and A1288:A1289 Interaction | Interacting Bases [1,3] | Pair Probability [[0.116980406,0.002286289,0.128092864,0.002286289,0.000000000],[0.238432839,0.010818673,0.211972452,0.002286289,0.000000000],[0.002286289,0.002286289,0.015616865,0.023612565,0.000000000],[0.022709642,0.002286289,0.010943960,0.207102000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1248 - A1288 tWH Interaction | Interacting Bases [2,3] | Pair Probability [[0.116980406,0.002286289,0.128092864,0.002286289,0.000000000],[0.238432839,0.010818673,0.211972452,0.002286289,0.000000000],[0.002286289,0.002286289,0.015616865,0.023612565,0.000000000],[0.022709642,0.002286289,0.010943960,0.207102000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1249 - A1288 tWH Interaction | Interacting Bases [1,4] | Pair Probability [[0.372110072,0.003623062,0.310683039,0.003623062,0.000000000],[0.127534032,0.013309690,0.020739161,0.003623062,0.000000000],[0.003623062,0.003623062,0.044878779,0.032327470,0.000000000],[0.017275422,0.003623062,0.021448740,0.017955228,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A1248 - A1289 tWH 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 [4] | Right Index [11] // Initial node A1250 - A1287 from junction FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Position [1] | Left Index [4] | Right Index [11] // 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 [5] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [5] | Right Index [11] // 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 [6] | Right Index [11] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [6] | Right Index [11] // 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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [6] | Right Index [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Position [2] | Left Index [6] | Right Index [10] // 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 [0.493381468,0.493381468,0.012635379,0.000601685] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [6] | Right Index [9] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.209900785,0.189444278,0.003757542,0.029684459,0.000000000],[0.026190026,0.016148501,0.011187579,0.015892215,0.000000000],[0.003757542,0.013137060,0.191703579,0.206023018,0.000000000],[0.017467990,0.015584336,0.018297597,0.031823494,0.000000000],[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 [6] | Right Index [9] // Basepair A1252 - A1285 tWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009722986,0.022602524,0.010807110,0.213946067,0.000000000],[0.018642384,0.008854915,0.200306720,0.011770232,0.000000000],[0.010724456,0.213953122,0.002148800,0.027678057,0.000000000],[0.199554445,0.012136228,0.023684855,0.013467100,0.000000000],[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 G1253 - C1284 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_52940.1:
> IL_52940.1 IL_1FJG_049 U 1247 G 1290 UACAAAG*CAAAAAG > IL_52940.1 IL_3U5F_076 G 1480 C 1527 GCCAGCGA*UUGUGAAAC