| 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 11 4 | 9 11 I | 10 12 5 | 11 12 I | 12 13 | 13 12 I | 14 12 6 | 15 11 I | 16 11 7 | 17 10 I | 18 9 8 | 19 8 I | 20 7 9 | 21 2 I | 22 2 10 | 23 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_25186.4_Instance_1 IL_25186.4,IL_7Q80_002,G14_C35 | G | A | C | C | C | G | A | C | A | A | C | |||||||||||||||||
| IL_25186.4_Sequence_1 IL_25186.47Q80_G14_C35 | G | A | C | C | C | * | G | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_25186.4_Instance_2 IL_25186.4,IL_3BNN_007,C5_G17 | C | A | C | C | C | G | A | C | A | A | G | |||||||||||||||||
| IL_25186.4_Sequence_2 IL_25186.43BNN_C5_G17 | C | A | C | C | C | * | G | A | C | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_25186.4_Instance_3 IL_25186.4,IL_3BNN_006,C5_G17 | C | A | C | C | C | G | A | C | A | A | G | |||||||||||||||||
| IL_25186.4_Sequence_3 IL_25186.43BNN_C5_G17 | C | A | C | C | C | * | G | A | C | A | A | G | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_25186.4_Instance_4 IL_25186.4,IL_8ZAU_002,G12_C38 | G | A | C | C | C | G | A | C | A | A | C | |||||||||||||||||
| IL_25186.4_Sequence_4 IL_25186.48ZAU_G12_C38 | G | A | C | C | C | * | G | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_25186.4_Instance_5 IL_25186.4,IL_7Q80_004,G14_C35 | G | A | C | C | C | G | A | C | A | A | C | |||||||||||||||||
| IL_25186.4_Sequence_5 IL_25186.47Q80_G14_C35 | G | A | C | C | C | * | G | A | C | A | A | C | true | 100 | 0 | 0 | 0.00 | |||||||||||
| IL_25186.4_Instance_6 IL_25186.4,IL_4WF9_116,C1511_G1570 | C | U | A | A | G | U | G | A | U | G | G | |||||||||||||||||
| IL_25186.4_Sequence_6 IL_25186.44WF9_C_1511_G_1570 | C | U | A | A | G | * | U | G | A | U | G | G | true | 45 | 0 | 0 | 10.26 |
1 9 s35 1 10 cWW 2 3 s35 3 4 s35 4 5 s35 4 7 cWW 5 6 cWW 6 7 s35 7 8 s35 8 9 s33 9 10 s55JAR3D SCFG/MRF model for IL_25186.4:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.009271545,0.017981432,0.010607783,0.192505806,0.000000000],[0.017981779,0.009265445,0.226529308,0.013026479,0.000000000],[0.010607796,0.226528663,0.002010668,0.024167927,0.000000000],[0.192506087,0.013026424,0.024168288,0.009814571,0.000000000],[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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.687500000,0.062500000,0.187500000,0.062500000,0.000000000] | Left Index [1] | Right Index [10] // Basepair G14 - C35 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.687500000,0.062500000,0.062500000,0.187500000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 7Q80|1|B|A|15 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 [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.687500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 7Q80|1|B|C|16 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 [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.687500000,0.062500000,0.062500000,0.187500000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 7Q80|1|C|A|33 InitialNode | Left Length Distribution [1.000000000] | 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 [4] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.687500000,0.062500000,0.062500000,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right for 7Q80|1|C|C|32 InitialNode | Left Length Distribution [1.000000000] | 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 [4] | Right Index [7] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010235899,0.013402768,0.044927279,0.028238513,0.000000000],[0.398656227,0.037567338,0.031924485,0.014551830,0.000000000],[0.013344848,0.026925523,0.003290246,0.013916712,0.000000000],[0.035480019,0.013261304,0.301083025,0.013193984,0.000000000],[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 [4] | Right Index [7] // Basepair C17 - A31 cWW BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008996772,0.016133374,0.010342897,0.187537126,0.000000000],[0.019128677,0.009162952,0.244316465,0.013010038,0.000000000],[0.010459051,0.191578047,0.001971467,0.050069857,0.000000000],[0.189968357,0.012534922,0.025255896,0.009534102,0.000000000],[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 [5] | Right Index [6] // Basepair C18 - G30 cWW HairpinNode | Num Bases [1] | Left Index [6] | Right Index [6] | 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_25186.4:
> IL_25186.4 7Q80 G 14 C 35 GACCC*GACAAC > IL_25186.4 3BNN C 5 G 17 CACCC*GACAAG > IL_25186.4 3BNN C 5 G 17 CACCC*GACAAG > IL_25186.4 8ZAU G 12 C 38 GACCC*GACAAC > IL_25186.4 7Q80 G 14 C 35 GACCC*GACAAC > IL_25186.4 4WF9 C 1511 G 1570 CUAAG*UGAUGG