| 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_66798.2_Instance_1 IL_66798.2,IL_9DFE_014,U606_G622 | U | U | A | A | G | C | G | G | A | G | ||||||||||||||||||
| IL_66798.2_Sequence_1 IL_66798.29DFE_U606_G622 | U | U | A | A | G | * | C | G | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_66798.2_Instance_2 IL_66798.2,IL_5J7L_258,U606_G622 | U | U | A | A | C | G | G | G | A | G | ||||||||||||||||||
| IL_66798.2_Sequence_2 IL_66798.25J7L_U606_G622 | U | U | A | A | C | * | G | G | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_66798.2_Instance_3 IL_66798.2,IL_7A0S_013,U616_G633 | U | U | A | A | G | C | G | G | A | G | ||||||||||||||||||
| IL_66798.2_Sequence_3 IL_66798.27A0S_U616_G633 | U | U | A | A | G | * | C | G | G | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| IL_66798.2_Instance_4 IL_66798.2,IL_4V9F_020,C663_G683 | C | U | A | A | C | G | G | G | A | G | ||||||||||||||||||
| IL_66798.2_Sequence_4 IL_66798.24V9F_C663_G683 | C | U | A | A | C | * | G | G | G | A | G | true | 94 | 0 | 0 | 0.83 | ||||||||||||
| IL_66798.2_Instance_5 IL_66798.2,IL_4WF9_019,U649_G667 | U | U | A | A | G | U | G | G | A | G | ||||||||||||||||||
| IL_66798.2_Sequence_5 IL_66798.24WF9_U649_G667 | U | U | A | A | G | * | U | G | G | A | G | true | 94 | 0 | 0 | 0.84 | ||||||||||||
| IL_66798.2_Instance_6 IL_66798.2,IL_4WF9_074,C1909_G1887 | C | G | A | A | U | A | G | G | A | G | ||||||||||||||||||
| IL_66798.2_Sequence_6 IL_66798.24WF9_C_1909_G_1887 | C | G | A | A | U | * | A | G | G | A | G | true | 85 | 0 | 0 | 2.19 |
1 8 perp 1 10 cWW 2 8 s53 3 4 s35 3 9 s55 4 5 s35 4 7 tHS 5 6 cWW 5 7 s55 6 7 s35 8 10 perp 9 10 s35 7 3 6BPh 8 7 6BPh 8 8 2BPh 4 7 6BRJAR3D SCFG/MRF model for IL_66798.2:
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 [10] // Initial node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.010273412,0.014456196,0.012675799,0.087674627,0.000000000],[0.200584829,0.021046069,0.113068351,0.014709460,0.000000000],[0.012915807,0.088952759,0.002791224,0.016939129,0.000000000],[0.119882746,0.013678686,0.258415347,0.011935558,0.000000000],[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 [10] // Basepair U606 - G622 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.062500000,0.062500000,0.187500000,0.687500000,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left for 9DFE|1|1A|U|607 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 [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left for 9DFE|1|1A|A|608 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 [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Position [2] | Left Index [4] | Right Index [9] // Fixed node on right for 9DFE|1|1A|A|621 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 [0.001689189,0.001689189,0.994932432,0.001689189,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right for 9DFE|1|1A|G|620 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 [[0.053122716,0.053517379,0.372759245,0.059299138,0.000000000],[0.056237554,0.056107331,0.003161555,0.055804425,0.000000000],[0.000637703,0.000637703,0.015455837,0.000637703,0.000000000],[0.003005495,0.000637703,0.268340811,0.000637703,0.000000000],[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 A609 - G619 tHS BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010170282,0.062415350,0.010957433,0.173387839,0.000000000],[0.017724023,0.009804871,0.188453779,0.012765899,0.000000000],[0.010911349,0.188871961,0.002188623,0.081274908,0.000000000],[0.176422830,0.012871605,0.026968536,0.014810709,0.000000000],[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 G610 - C618 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_66798.2:
> IL_66798.2 9DFE U 606 G 622 UUAAG*CGGAG > IL_66798.2 5J7L U 606 G 622 UUAAC*GGGAG > IL_66798.2 7A0S U 616 G 633 UUAAG*CGGAG > IL_66798.2 4V9F C 663 G 683 CUAAC*GGGAG > IL_66798.2 4WF9 U 649 G 667 UUAAG*UGGAG > IL_66798.2 4WF9 C 1909 G 1887 CGAAU*AGGAG