| 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 7 3 | 7 7 I | 8 8 | 9 7 I | 10 7 4 | 11 6 I | 12 12 5 | 13 12 I | 14 15 6 | 15 15 I | 16 16 7 | 17 17 I | 18 20 8 | 19 20 I | 20 21 9 | 21 21 I | 22 22 | 23 21 I | 24 21 10 | 25 20 I | 26 20 11 | 27 19 I | 28 18 12 | 29 15 I | 30 15 13 | 31 14 I | 32 13 14 | 33 12 I | 34 12 15 | 35 11 I | 36 24 16 | 37 25 I | 38 26 17 | 39 27 I | 40 28 18 | 41 29 I | 42 30 19 | 43 31 I | 44 32 20 | 45 32 I | 46 33 | 47 32 I | 48 32 21 | 49 2 I | 50 2 22 | 51 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| J4_61885.2_Instance_1 J4_61885.2,J4_4LFB_003,G575_C880 | G | G | G | C | G | A | A | A | G | C | C | C | U | A | A | A | C | G | A | U | G | C | C | |||||||||||||||||||||||||||||||||
| J4_61885.2_Sequence_1 J4_61885.24LFB_G575_C880 | G | G | G | * | C | G | A | A | A | G | * | C | C | C | U | A | A | A | C | G | A | U | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||||
| J4_61885.2_Instance_2 J4_61885.2,J4_6CZR_013,G559_C858 | G | G | G | C | G | A | A | A | G | C | C | C | U | A | A | A | C | G | A | U | G | C | C | |||||||||||||||||||||||||||||||||
| J4_61885.2_Sequence_2 J4_61885.26CZR_G559_C858 | G | G | G | * | C | G | A | A | A | G | * | C | C | C | U | A | A | A | C | G | A | U | G | * | C | C | true | 100 | 0 | 0 | 0.00 | |||||||||||||||||||||||||
| J4_61885.2_Instance_3 J4_61885.2,J4_5J7L_003,G575_C880 | G | C | G | C | G | A | A | A | G | C | C | G | U | A | A | A | C | G | A | U | G | C | C | |||||||||||||||||||||||||||||||||
| J4_61885.2_Sequence_3 J4_61885.25J7L_G575_C880 | G | C | G | * | C | G | A | A | A | G | * | C | C | G | U | A | A | A | C | G | A | U | G | * | C | C | true | 96 | 0 | 0 | 1.02 | |||||||||||||||||||||||||
| J4_61885.2_Instance_4 J4_61885.2,J4_4V88_024,A622_U1104 | A | A | G | C | G | A | A | A | G | C | C | A | U | A | A | A | C | U | A | U | G | U | U | |||||||||||||||||||||||||||||||||
| J4_61885.2_Sequence_4 J4_61885.24V88_A622_U_1104 | A | A | G | * | C | G | A | A | A | G | * | C | C | A | U | A | A | A | C | U | A | U | G | * | U | U | true | 90 | 0 | 0 | 2.55 |
1 20 s35 1 22 cWW 3 4 cWW 3 5 s55 3 15 s53 4 5 s35 5 12 s33 5 15 cSS 6 7 s35 6 13 tHW 6 14 s55 7 8 s35 7 13 s55 8 9 s35 8 11 bif 9 10 cWW 9 11 s55 10 11 s35 11 12 s35 13 15 s35 14 15 s35 16 18 s55 17 19 s33 20 21 cWW 20 22 s55 21 22 s35 5 13 6BPh 15 13 6BPh 15 14 7BPh 19 18 7BPh 5 12 6BRJAR3D SCFG/MRF model for J4_61885.2:
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 [22] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | 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 [0.995990040,0.003999960,0.000010000] | 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 [22] // Basepair G575 - C880 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.250000000,0.416666667,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [21] // Fixed node on left for 4LFB|1|A|G|576 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [21] // New Initial node after Fixed node JunctionNode | Branches [2] | Left Index [3] | Right Index [21] // Junction node G577 - C879 ID J6160 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 [3] | Right Index [4] // Initial node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [3] | Right Index [4] // Basepair G577 - C764 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 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 [5] | Right Index [21] // Initial node 4LFB|1|A|G|765 - 4LFB|1|A|C|879 from node JunctionNode | Branches [2] | Left Index [5] | Right Index [21] // Junction node G765 - C879 ID J4732 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 [5] | Right Index [15] // Initial node BasepairNode | Deletion Probability [0.0000001215781528] | Pair Probability [[0.085447440,0.003841308,0.003932561,0.003631348,0.000000000],[0.088789616,0.004187355,0.000168132,0.000572732,0.000000000],[0.685058755,0.001202885,0.002667015,0.021395690,0.000000000],[0.087155244,0.003856303,0.003886910,0.004206705,0.000000000],[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 [0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Left Index [5] | Right Index [15] // Basepair G765 - A816 cSS FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [2] | Left Index [6] | Right Index [14] // Fixed node on right for 4LFB|1|A|A|814 InitialNode | Left Length Distribution [1.000000000] | 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 [6] | Right Index [13] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.018414538,0.040981170,0.004075167,0.445978203,0.000000000],[0.004075167,0.328380556,0.009768444,0.004075167,0.000000000],[0.019126511,0.004075167,0.030991298,0.023643628,0.000000000],[0.004075167,0.004075167,0.018124938,0.040139714,0.000000000],[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 [6] | Right Index [13] // Basepair A766 - U813 tHW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [7] | Right Index [12] // Fixed node on left for 4LFB|1|A|A|767 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [8] | Right Index [12] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.416666667,0.250000000,0.083333333,0.000000000] | Position [2] | Left Index [8] | Right Index [12] // Fixed node on right for 4LFB|1|A|C|812 InitialNode | Left Length Distribution [1.000000000] | 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 [8] | Right Index [11] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.027044640,0.729367860,0.006598890,0.006598890,0.000000000],[0.030381196,0.077281953,0.006598890,0.006598890,0.000000000],[0.006598890,0.006598890,0.027690098,0.006598890,0.000000000],[0.006598890,0.006598890,0.042245358,0.006598890,0.000000000],[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 [8] | Right Index [11] // Basepair A768 - C811 bif BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.009546506,0.019881954,0.010870922,0.197449200,0.000000000],[0.016768697,0.009361308,0.199122279,0.013028540,0.000000000],[0.010750195,0.243371713,0.002049102,0.026250458,0.000000000],[0.194922229,0.013522366,0.023009709,0.010094826,0.000000000],[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 [9] | Right Index [10] // Basepair G769 - C810 cWW HairpinNode | Num Bases [1] | Left Index [10] | Right Index [10] | 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 [16] | Right Index [21] // Initial node 4LFB|1|A|C|817 - 4LFB|1|A|C|879 from node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.750000000,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [16] | Right Index [21] // Fixed node on left for 4LFB|1|A|A|816 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [17] | Right Index [21] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.083333333,0.583333333,0.250000000,0.000000000] | Position [1] | Left Index [17] | Right Index [21] // Fixed node on left for 4LFB|1|A|C|817 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [18] | Right Index [21] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.750000000,0.083333333,0.083333333,0.083333333,0.000000000] | Position [1] | Left Index [18] | Right Index [21] // Fixed node on left for 4LFB|1|A|G|818 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [19] | Right Index [21] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.016666667,0.016666667,0.016666667,0.950000000,0.000000000] | Position [1] | Left Index [19] | Right Index [21] // Fixed node on left for 4LFB|1|A|A|819 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [20] | Right Index [21] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000224863733088] | Pair Probability [[0.011043683,0.087705864,0.011663765,0.168825951,0.000000000],[0.015941238,0.010156843,0.158274510,0.013303388,0.000000000],[0.011498012,0.192719706,0.002332326,0.108853206,0.000000000],[0.155160397,0.013999784,0.020787547,0.017733780,0.000000000],[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 [20] | Right Index [21] // Basepair G821 - C879 cWW HairpinNode | Num Bases [1] | Left Index [21] | Right Index [21] | 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_61885.2:
> J4_61885.2 4LFB G 575 C 880 GGG*CGAAAG*CCCUAAACGAUG*CC > J4_61885.2 6CZR G 559 C 858 GGG*CGAAAG*CCCUAAACGAUG*CC > J4_61885.2 5J7L G 575 C 880 GCG*CGAAAG*CCGUAAACGAUG*CC > J4_61885.2 4V88 A 622 U 1104 AAG*CGAAAG*CCAUAAACUAUG*UU