| 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 | 7 4 I | 8 3 3 | 9 3 I | 10 3 4 | 11 3 I | 12 3 5 | 13 2 I | 14 2 6 | 15 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_73000.2_Instance_1 IL_73000.2_IL_3UCZ_004_G76_C64 | G | U | A | A | A | C | ||||||||||||||
| IL_73000.2_Sequence_1 IL_73000.2_IL_3UCZ_004_G76_C64 | G | U | * | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_73000.2_Instance_2 IL_73000.2_IL_3IWN_005_G71_C54 | G | U | A | A | A | C | ||||||||||||||
| IL_73000.2_Sequence_2 IL_73000.2_IL_3IWN_005_G71_C54 | G | U | * | A | A | A | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| IL_73000.2_Instance_3 IL_73000.2_IL_2AW7_054_G1142_C1132 | G | G | C | A | G | C | ||||||||||||||
| IL_73000.2_Sequence_3 IL_73000.2_IL_2AW7_054_G_1142_C_1132 | G | G | * | C | A | G | C | true | 94 | 0 | 0 | 0.60 | ||||||||
| IL_73000.2_Instance_4 IL_73000.2_IL_2AW7_013_G213_C206 | G | C | G | G | A | C | ||||||||||||||
| IL_73000.2_Sequence_4 IL_73000.2_IL_2AW7_013_G213_C206 | G | C | * | G | G | A | C | true | 92 | 0 | 0 | 0.79 | ||||||||
| IL_73000.2_Instance_5 IL_73000.2_IL_4A1B_066_G1539_C1531 | G | U | U | A | G | A | A | C | ||||||||||||
| IL_73000.2_Sequence_5 IL_73000.2_IL_4A1B_066_G_1539_C_1531 | G | U | U | * | A | G | A | A | C | true | 60 | 0 | 0 | 3.76 | ||||||
| IL_73000.2_Instance_6 IL_73000.2_IL_2QBG_003_C30_G54 | C | C | G | A | A | G | ||||||||||||||
| IL_73000.2_Sequence_6 IL_73000.2_IL_2QBG_003_C30_G54 | C | C | * | G | A | A | G | true | 93 | 0 | 0 | 0.67 | ||||||||
| IL_73000.2_Instance_7 IL_73000.2_IL_2AW7_044_G933_C1384 | G | C | A | U | U | C | C | C | ||||||||||||
| IL_73000.2_Sequence_7 IL_73000.2_IL_2AW7_044_G933_C_1384 | G | C | A | * | U | U | C | C | C | true | 44 | 0 | 0 | 5.32 |
1 2 s35 1 6 cWW 2 3 cWW 2 5 cSW 3 4 cSH 4 5 s35 5 6 s35JAR3D SCFG/MRF model for IL_73000.2:
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 [6] // Initial node G76 - C64 from junction BasepairNode | Deletion Probability [0.0000052393233623] | Pair Probability [[0.009696313,0.019313569,0.011232880,0.184287162,0.000000000],[0.016884566,0.008035654,0.208890895,0.012733823,0.000000000],[0.011131706,0.260092205,0.002049121,0.025767468,0.000000000],[0.183526462,0.013182737,0.023188255,0.009987184,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair G76 - C64 cWW ClusterNode | Deletion Probability [0.0000000001323925] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.062935737109612] // Cluster node U77:U77 and A61:A63 Interaction | Interacting Bases [1,2] | Pair Probability [[0.009104522,0.019068653,0.010130221,0.202038967,0.000000000],[0.020744927,0.008639905,0.211004470,0.011238095,0.000000000],[0.010155036,0.200458510,0.002050733,0.023679133,0.000000000],[0.223086224,0.011128398,0.025343219,0.012128987,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U77 - A61 cWW Interaction | Interacting Bases [1,4] | Pair Probability [[0.126758533,0.055585452,0.014037661,0.008663852,0.000000000],[0.168755935,0.040188393,0.013939587,0.009789708,0.000000000],[0.117302516,0.039733096,0.144249774,0.007108942,0.000000000],[0.194184319,0.042380809,0.009741284,0.007580138,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U77 - A63 cSW Interaction | Interacting Bases [2,3] | Pair Probability [[0.119225934,0.088672012,0.046358530,0.009822107,0.000000000],[0.098358845,0.084485776,0.002105316,0.085313352,0.000000000],[0.092777380,0.010484959,0.066131830,0.084785516,0.000000000],[0.029200906,0.097227503,0.002105316,0.082944717,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A61 - A62 cSH Insertion | Location [2] | Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node 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 [3] | Right Index [2] // New Initial node after Cluster HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | 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_73000.2:
> IL_73000.2 IL_3UCZ_004 G 76 C 64 GU*AAAC > IL_73000.2 IL_3IWN_005 G 71 C 54 GU*AAAC > IL_73000.2 IL_2AW7_054 G 1142 C 1132 GG*CAGC > IL_73000.2 IL_2AW7_013 G 213 C 206 GC*GGAC > IL_73000.2 IL_4A1B_066 G 1539 C 1531 GUU*AGAAC > IL_73000.2 IL_2QBG_003 C 30 G 54 CC*GAAG > IL_73000.2 IL_2AW7_044 G 933 C 1384 GCA*UUCCC