| 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 5 2 | 5 5 I | 6 6 | 7 5 I | 8 5 3 | 9 4 I | 10 10 4 | 11 10 I | 12 11 | 13 10 I | 14 10 5 | 15 9 I | 16 13 6 | 17 13 I | 18 14 | 19 13 I | 20 13 7 | 21 2 I | 22 2 8 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_78628.1_Instance_1 J4_78628.1,J4_5J7L_024,G1444_C1547 | G | G | U | U | A | C | G | C | ||||||||||||||||||||
| J4_78628.1_Sequence_1 J4_78628.15J7L_G_1444_C_1547 | G | G | * | U | U | * | A | C | * | G | C | true | 100 | 0 | 0 | 0.02 | ||||||||||||
| J4_78628.1_Instance_2 J4_78628.1,J4_5TBW_005,A1752_U1694 | A | G | U | C | G | G | C | U | ||||||||||||||||||||
| J4_78628.1_Sequence_2 J4_78628.15TBW_A_1752_U_1694 | A | G | * | U | C | * | G | G | * | C | U | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| J4_78628.1_Instance_3 J4_78628.1,J4_4Y4O_019,G1444_C1547 | G | A | C | G | C | G | G | C | C | |||||||||||||||||||
| J4_78628.1_Sequence_3 J4_78628.14Y4O_G_1444_C_1547 | G | A | C | * | G | C | * | G | G | * | C | C | true | 78 | 0 | 0 | 2.05 | |||||||||||
| J4_78628.1_Instance_4 J4_78628.1,J4_4V9F_006,G1627_C1570 | G | G | C | G | C | G | U | C | ||||||||||||||||||||
| J4_78628.1_Sequence_4 J4_78628.14V9F_G_1627_C_1570 | G | G | * | C | G | * | C | G | * | U | C | true | 91 | 0 | 0 | 0.84 |
1 2 s35 1 8 cWW 2 3 cWW 2 8 s55 3 8 s35 4 5 cWW 4 6 s55 4 7 s53 5 6 s35 6 7 cWWJAR3D SCFG/MRF model for J4_78628.1:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000060823043662] | Pair Probability [[0.009435981,0.020308281,0.010584118,0.207749754,0.000000000],[0.016871843,0.009369986,0.196949712,0.012311312,0.000000000],[0.010488840,0.230753978,0.002037301,0.032735453,0.000000000],[0.194255155,0.012845795,0.022899797,0.010402692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.741082411,0.255227552,0.003536285,0.000153752] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | 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 [8] // Basepair G1444 - C1547 cWW JunctionNode | Branches [2] | Left Index [2] | Right Index [7] // Junction node G1445 - G1546 ID J2289 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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 [3] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.012492529,0.154752412,0.012427037,0.139582023,0.000000000],[0.015893222,0.010993538,0.128500730,0.013702461,0.000000000],[0.012276627,0.131016641,0.002615667,0.190647073,0.000000000],[0.116041515,0.014354485,0.019377064,0.025326977,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [3] // Basepair G1445 - U1466 cWW 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 truncation InitialNode | Left Length Distribution [1.000000000] | 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 [7] // Initial node 5J7L|1|DA|U|1467 - 5J7L|1|DA|G|1546 from node JunctionNode | Branches [2] | Left Index [4] | Right Index [7] // Junction node U1467 - G1546 ID J9133 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | 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] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009278367,0.017658581,0.010523925,0.194981980,0.000000000],[0.019540415,0.009513951,0.219788080,0.012727977,0.000000000],[0.010558860,0.208106937,0.002038293,0.023721161,0.000000000],[0.207216391,0.012440103,0.031948050,0.009956928,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [5] // Basepair U1467 - A1525 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 truncation InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [6] | Right Index [7] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.010995352,0.086928502,0.011634194,0.168205272,0.000000000],[0.016720680,0.010198002,0.169348499,0.013427613,0.000000000],[0.011528810,0.181668648,0.002332442,0.108044325,0.000000000],[0.155803347,0.013877067,0.021599225,0.017688023,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.990049834,0.009900498,0.000049502,0.000000165] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [6] | Right Index [7] // Basepair C1526 - G1546 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 J4_78628.1:
> J4_78628.1 5J7L G 1444 C 1547 GG*UU*AC*GC > J4_78628.1 5TBW A 1752 U 1694 AG*UC*GG*CU > J4_78628.1 4Y4O G 1444 C 1547 GAC*GC*GG*CC > J4_78628.1 4V9F G 1627 C 1570 GG*CG*CG*UC