| 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 5 I | 8 6 4 | 9 6 I | 10 7 | 11 6 I | 12 6 5 | 13 5 I | 14 4 6 | 15 4 I | 16 4 7 | 17 3 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_54966.1_Instance_1 IL_54966.1_IL_1FJG_055_G1401_C1501 | G | C | C | C | G | U | A | A | C | |||||||||||||||||
| IL_54966.1_Sequence_1 IL_54966.1_IL_1FJG_055_G_1401_C_1501 | G | C | C | C | * | G | U | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_54966.1_Instance_2 IL_54966.1_IL_2AW7_061_G1401_C1501 | G | C | C | C | G | U | A | A | C | |||||||||||||||||
| IL_54966.1_Sequence_2 IL_54966.1_IL_2AW7_061_G_1401_C_1501 | G | C | C | C | * | G | U | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_54966.1_Instance_3 IL_54966.1_IL_3U5F_081_G1638_C1764 | G | C | C | C | G | U | A | A | C | |||||||||||||||||
| IL_54966.1_Sequence_3 IL_54966.1_IL_3U5F_081_G_1638_C_1764 | G | C | C | C | * | G | U | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_54966.1_Instance_4 IL_54966.1_IL_4BPP_081_G1610_C1717 | G | C | C | C | G | U | A | A | C | |||||||||||||||||
| IL_54966.1_Sequence_4 IL_54966.1_IL_4BPP_081_G_1610_C_1717 | G | C | C | C | * | G | U | A | A | C | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 8 cWW 3 4 s35 3 7 cSW 4 5 cWW 4 7 s55 5 6 s35 6 7 cSH 7 8 s35 8 9 s35JAR3D SCFG/MRF model for IL_54966.1:
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 [9] // Initial node G1401 - C1501 from junction BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009999033,0.020370037,0.011577394,0.189754219,0.000000000],[0.016871198,0.008244913,0.204374808,0.013008374,0.000000000],[0.011431659,0.249278495,0.002108170,0.027040831,0.000000000],[0.188658474,0.013655008,0.023325621,0.010301767,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G1401 - C1501 cWW BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.011872772,0.014708582,0.014301144,0.033757857,0.000000000],[0.399542582,0.017945751,0.034889197,0.016036878,0.000000000],[0.014645019,0.028896488,0.003610810,0.015133880,0.000000000],[0.041074697,0.014455142,0.324408656,0.014720545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [8] // Basepair C1402 - A1500 cWW ClusterNode | Deletion Probability [0.0000001250000000] | Num Left Bases [1] | Num Right Bases [2] | Left Index [3] | Right Index [7] | Norm Constant [0.326407563543262] // Cluster node C1403:C1403 and U1498:A1499 Interaction | Interacting Bases [1,3] | Pair Probability [[0.177419266,0.022538031,0.009786791,0.007644646,0.000000000],[0.238046717,0.018024818,0.009854628,0.008394557,0.000000000],[0.172050331,0.019796743,0.093017756,0.006569858,0.000000000],[0.180923828,0.019886693,0.009052772,0.006992564,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1403 - A1499 cSW Interaction | Interacting Bases [2,3] | Pair Probability [[0.021745117,0.127570845,0.025990805,0.016040998,0.000000000],[0.031117562,0.014978621,0.002550147,0.017709157,0.000000000],[0.011100813,0.205739968,0.053341346,0.018363188,0.000000000],[0.293476277,0.144133058,0.002550147,0.013591951,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U1498 - A1499 cSH InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009837906,0.016874612,0.011433973,0.188696651,0.000000000],[0.020374159,0.008402684,0.249321155,0.013657771,0.000000000],[0.011579737,0.204416164,0.002108596,0.023330341,0.000000000],[0.189792617,0.013011006,0.027046303,0.010116326,0.000000000],[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 [4] | Right Index [5] // Basepair C1404 - G1497 cWW HairpinNode | Num Bases [1] | Left Index [5] | Right Index [5] | 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_54966.1:
> IL_54966.1 IL_1FJG_055 G 1401 C 1501 GCCC*GUAAC > IL_54966.1 IL_2AW7_061 G 1401 C 1501 GCCC*GUAAC > IL_54966.1 IL_3U5F_081 G 1638 C 1764 GCCC*GUAAC > IL_54966.1 IL_4BPP_081 G 1610 C 1717 GCCC*GUAAC