| 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 5 I | 8 6 | 9 5 I | 10 5 4 | 11 4 I | 12 3 5 | 13 3 I | 14 3 6 | 15 3 I | 16 3 7 | 17 2 I | 18 2 8 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_25380.1_Instance_1 IL_25380.1_IL_4GXY_009_C105_G126 | C | A | C | G | G | A | A | G | ||||||||||||||||
| IL_25380.1_Sequence_1 IL_25380.1_IL_4GXY_009_C105_G126 | C | A | C | * | G | G | A | A | G | true | 75 | 0 | 0 | 2.66 | ||||||||||
| IL_25380.1_Instance_2 IL_25380.1_IL_4GMA_007_C113_G132 | C | A | C | G | G | A | A | G | ||||||||||||||||
| IL_25380.1_Sequence_2 IL_25380.1_IL_4GMA_007_C113_G132 | C | A | C | * | G | G | A | A | G | true | 75 | 0 | 0 | 2.66 | ||||||||||
| IL_25380.1_Instance_3 IL_25380.1_IL_4BPP_071_A1317_U1350 | A | CU | A | G | C | U | U | C | U | |||||||||||||||
| IL_25380.1_Sequence_3 IL_25380.1_IL_4BPP_071_A_1317_U_1350 | A | CU | A | G | * | C | U | U | C | U | true | 57 | 0 | 0 | 4.64 | |||||||||
| IL_25380.1_Instance_4 IL_25380.1_IL_4IOA_088_A2438_U2472 | A | U | C | G | G | U | U | U | ||||||||||||||||
| IL_25380.1_Sequence_4 IL_25380.1_IL_4IOA_088_A_2438_U_2472 | A | U | C | * | G | G | U | U | U | true | 100 | 0 | 0 | 0.00 | ||||||||||
| IL_25380.1_Instance_5 IL_25380.1_IL_2XXA_009_G10_C93 | G | U | G | C | C | U | U | C | ||||||||||||||||
| IL_25380.1_Sequence_5 IL_25380.1_IL_2XXA_009_G10_C93 | G | U | G | * | C | C | U | U | C | true | 100 | 0 | 0 | 0.02 | ||||||||||
| IL_25380.1_Instance_6 IL_25380.1_IL_2QBG_093_A2459_U2493 | A | U | A | U | G | U | U | U | ||||||||||||||||
| IL_25380.1_Sequence_6 IL_25380.1_IL_2QBG_093_A_2459_U_2493 | A | U | A | * | U | G | U | U | U | true | 99 | 0 | 0 | 0.14 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cWW 3 4 cWW 4 5 s35 5 7 cSH 6 7 s35 7 8 s35JAR3D SCFG/MRF model for IL_25380.1:
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 [8] // Initial node C105 - G126 from junction BasepairNode | Deletion Probability [0.0000040113606825] | Pair Probability [[0.009303385,0.020606440,0.010352389,0.224394684,0.000000000],[0.019084521,0.008572365,0.213736718,0.011538453,0.000000000],[0.010368187,0.203786078,0.002067853,0.025420108,0.000000000],[0.192395003,0.011467640,0.024007914,0.012898260,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.824969064,0.008249691,0.165337550,0.001374948,0.000068747] | 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 [8] // Basepair C105 - G126 cWW ClusterNode | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [7] | Norm Constant [0.325985083110521] // Cluster node A106:A106 and G123:A125 Interaction | Interacting Bases [1,4] | Pair Probability [[0.090273333,0.187976707,0.013697566,0.032978943,0.000000000],[0.017577621,0.017891685,0.020685705,0.015101851,0.000000000],[0.013432372,0.021069153,0.004311624,0.043901633,0.000000000],[0.027693624,0.016392876,0.017551006,0.459464302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A106 - A125 cWW Interaction | Interacting Bases [2,4] | Pair Probability [[0.094625064,0.099445771,0.005326262,0.004472504,0.000000000],[0.092560928,0.100307341,0.001118543,0.140439759,0.000000000],[0.083930061,0.005637867,0.010582824,0.124852072,0.000000000],[0.025988045,0.109101383,0.001118543,0.100493033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G123 - A125 cSH Interaction | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A124 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 [4] // New Initial node after Cluster BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009579898,0.018858927,0.010968709,0.198510678,0.000000000],[0.018733316,0.008310552,0.229411558,0.012602551,0.000000000],[0.010989873,0.219102584,0.002068376,0.024744711,0.000000000],[0.187963655,0.012508405,0.024679279,0.010966928,0.000000000],[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 [3] | Right Index [4] // Basepair C107 - G122 cWW HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | 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_25380.1:
> IL_25380.1 IL_4GXY_009 C 105 G 126 CAC*GGAAG > IL_25380.1 IL_4GMA_007 C 113 G 132 CAC*GGAAG > IL_25380.1 IL_4BPP_071 A 1317 U 1350 ACUAG*CUUCU > IL_25380.1 IL_4IOA_088 A 2438 U 2472 AUC*GGUUU > IL_25380.1 IL_2XXA_009 G 10 C 93 GUG*CCUUC > IL_25380.1 IL_2QBG_093 A 2459 U 2493 AUA*UGUUU