| 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 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 4 I | 12 5 6 | 13 5 I | 14 6 | 15 5 I | 16 5 7 | 17 4 I | 18 3 8 | 19 2 I | 20 2 9 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_97273.1_Instance_1 IL_97273.1,IL_8P9A_423,G985_C1016 | G | G | G | A | U | C | G | U | C | |||||||||||||||||
| IL_97273.1_Sequence_1 IL_97273.18P9A_G985_C_1016 | G | G | G | A | U | C | * | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_97273.1_Instance_2 IL_97273.1,IL_8CRE_437,G970_C1001 | G | G | G | A | U | C | G | U | C | |||||||||||||||||
| IL_97273.1_Sequence_2 IL_97273.18CRE_G970_C_1001 | G | G | G | A | U | C | * | G | U | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_97273.1_Instance_3 IL_97273.1,IL_3AGV_005,G4_C20 | G | G | U | G | C | U | A | A | C | |||||||||||||||||
| IL_97273.1_Sequence_3 IL_97273.13AGV_G4_C20 | G | G | U | G | C | U | * | A | A | C | true | 79 | 0 | 0 | 2.98 |
1 2 s35 1 9 cWW 2 3 s35 2 8 tSH 2 9 s55 4 5 s35 5 6 s35 5 8 cWW 6 7 cWW 7 8 s35 8 9 perp 9 8 7BPhJAR3D SCFG/MRF model for IL_97273.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices InitialNode | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [9] // Initial node BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.003786762,0.055205280,0.004312111,0.078321123,0.000000000],[0.006651550,0.025993100,0.078984774,0.005167961,0.000000000],[0.004264222,0.598090606,0.000812806,0.010412629,0.000000000],[0.077318762,0.037546914,0.009127139,0.004004261,0.000000000],[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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G985 - C1016 cWW ClusterNode | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [2] | Right Index [8] | Norm Constant [0.267312138553150] // Cluster node 8P9A|1|sR|G|986:8P9A|1|sR|U|989 and 8P9A|1|sR|U|1015:8P9A|1|sR|U|1015 Interaction | Interacting Bases [1,5] | Pair Probability [[0.078297448,0.088009755,0.001789645,0.009995940,0.000000000],[0.068138988,0.070487675,0.001789645,0.001789645,0.000000000],[0.171259614,0.001789645,0.011370149,0.234961525,0.000000000],[0.154937097,0.101803936,0.001789645,0.001789645,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|G|986 - 8P9A|1|sR|U|1015 tSH Interaction | Interacting Bases [4,5] | Pair Probability [[0.014550416,0.266872370,0.012991067,0.022689713,0.000000000],[0.072022486,0.017340010,0.019394286,0.014261191,0.000000000],[0.012719729,0.019756895,0.004010360,0.051233113,0.000000000],[0.019820977,0.015444859,0.016439019,0.420453509,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 8P9A|1|sR|U|989 - 8P9A|1|sR|U|1015 cWW Interaction | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|sR|G|987 Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 8P9A|1|sR|A|988 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008994277,0.016128899,0.010340028,0.187485104,0.000000000],[0.019123371,0.009160410,0.216509443,0.013006429,0.000000000],[0.010456150,0.191524904,0.001970920,0.022131789,0.000000000],[0.245856484,0.012531445,0.025248890,0.009531458,0.000000000],[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 [6] | Right Index [7] // Basepair C990 - G1014 cWW HairpinNode | Num Bases [1] | Left Index [7] | Right Index [7] | 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_97273.1:
> IL_97273.1 8P9A G 985 C 1016 GGGAUC*GUC > IL_97273.1 8CRE G 970 C 1001 GGGAUC*GUC > IL_97273.1 3AGV G 4 C 20 GGUGCU*AAC