| 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 6 I | 8 7 4 | 9 7 I | 10 8 | 11 7 I | 12 7 5 | 13 4 I | 14 3 6 | 15 3 I | 16 3 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_92114.3_Instance_1 IL_92114.3_IL_1GID_007_U247_G227 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_1 IL_92114.3_IL_1GID_007_U247_G227 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_2 IL_92114.3_IL_1GID_014_U247_G227 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_2 IL_92114.3_IL_1GID_014_U247_G227 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_3 IL_92114.3_IL_3T4B_002_U17_G6 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_3 IL_92114.3_IL_3T4B_002_U17_G6 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_4 IL_92114.3_IL_1X8W_007_U247_G227 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_4 IL_92114.3_IL_1X8W_007_U247_G227 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_5 IL_92114.3_IL_1U6B_003_U80_G65 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_5 IL_92114.3_IL_1U6B_003_U80_G65 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_6 IL_92114.3_IL_2Y9B_003_U846_G860 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_6 IL_92114.3_IL_2Y9B_003_U846_G860 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_7 IL_92114.3_IL_4FAW_013_U332_G350 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_7 IL_92114.3_IL_4FAW_013_U332_G350 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_92114.3_Instance_8 IL_92114.3_IL_1NBS_008_U159_G150 | U | A | U | G | C | U | A | C | G | |||||||||||||||||
| IL_92114.3_Sequence_8 IL_92114.3_IL_1NBS_008_U159_G150 | U | A | U | G | * | C | U | A | C | G | true | 98 | 0 | 0 | 0.31 | |||||||||||
| IL_92114.3_Instance_9 IL_92114.3_IL_1KXK_002_U54_G19 | U | A | U | G | C | U | A | A | G | |||||||||||||||||
| IL_92114.3_Sequence_9 IL_92114.3_IL_1KXK_002_U54_G19 | U | A | U | G | * | C | U | A | A | G | true | 100 | 0 | 0 | 0.00 |
1 7 s33 1 9 cWW 2 4 s35 2 6 tHW 2 7 s55 2 8 s55 4 5 cWW 4 6 s55 5 6 s35 6 7 s35 7 8 cSH 8 9 s35 7 2 6BPhJAR3D SCFG/MRF model for IL_92114.3:
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 U247 - G227 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012182087,0.013837615,0.014555837,0.036251835,0.000000000],[0.296622029,0.015030447,0.042347731,0.016343772,0.000000000],[0.014885271,0.036529467,0.003301533,0.014494165,0.000000000],[0.042704523,0.014752267,0.412722117,0.013439304,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | 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 [9] // Basepair U247 - G227 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node A248:A248 and U224:A226 Interaction | Interacting Bases [1,2] | Pair Probability [[0.024303886,0.050629295,0.005097095,0.592278346,0.000000000],[0.005097095,0.042318173,0.005097095,0.005097095,0.000000000],[0.025002371,0.033833725,0.059652023,0.062880524,0.000000000],[0.005097095,0.005097095,0.023776461,0.054742624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A248 - U224 tHW Interaction | Interacting Bases [3,4] | Pair Probability [[0.410544386,0.302233525,0.014876145,0.012827737,0.000000000],[0.042406868,0.039953161,0.000472966,0.041617784,0.000000000],[0.002226097,0.002186075,0.002779584,0.039725290,0.000000000],[0.006415640,0.041366531,0.000472966,0.039895244,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A225 - A226 cSH InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // Initial node U249 - C223 from junction FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.045454545,0.045454545,0.863636364,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // Fixed node on left InitialNode | Left Length Distribution [0.997990020,0.001999980,0.000010000] | 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 [4] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009540362,0.019435632,0.011046321,0.181049897,0.000000000],[0.016097290,0.007866706,0.194999817,0.012411659,0.000000000],[0.010907271,0.283715261,0.002011465,0.025800426,0.000000000],[0.180004416,0.013028632,0.022255638,0.009829209,0.000000000],[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 G250 - C223 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_92114.3:
> IL_92114.3 IL_1GID_007 U 247 G 227 UAUG*CUAAG > IL_92114.3 IL_1GID_014 U 247 G 227 UAUG*CUAAG > IL_92114.3 IL_3T4B_002 U 17 G 6 UAUG*CUAAG > IL_92114.3 IL_1X8W_007 U 247 G 227 UAUG*CUAAG > IL_92114.3 IL_1U6B_003 U 80 G 65 UAUG*CUAAG > IL_92114.3 IL_2Y9B_003 U 846 G 860 UAUG*CUAAG > IL_92114.3 IL_4FAW_013 U 332 G 350 UAUG*CUAAG > IL_92114.3 IL_1NBS_008 U 159 G 150 UAUG*CUACG > IL_92114.3 IL_1KXK_002 U 54 G 19 UAUG*CUAAG