| 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 3 I | 6 4 3 | 7 5 I | 8 8 4 | 9 8 I | 10 9 5 | 11 9 I | 12 10 6 | 13 10 I | 14 11 | 15 10 I | 16 10 7 | 17 9 I | 18 9 8 | 19 8 I | 20 8 9 | 21 7 I | 22 6 10 | 23 3 I | 24 3 11 | 25 2 I | 26 2 12 | 27 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| IL_80494.2_Instance_1 IL_80494.2_IL_3P49_012_G116_C138 | G | C | A | A | A | G | C | C | U | A | A | A | C | |||||||||||||||||||
| IL_80494.2_Sequence_1 IL_80494.2_IL_3P49_012_G116_C138 | G | C | A | A | A | G | * | C | C | U | A | A | A | C | true | 97 | 0 | 0 | 0.58 | |||||||||||||
| IL_80494.2_Instance_2 IL_80494.2_IL_1S72_057_C1578_G1618 | C | C | A | A | C | U | A | C | G | A | A | C | G | |||||||||||||||||||
| IL_80494.2_Sequence_2 IL_80494.2_IL_1S72_057_C_1578_G_1618 | C | C | A | A | C | U | * | A | C | G | A | A | C | G | true | 100 | 0 | 0 | 0.00 | |||||||||||||
| IL_80494.2_Instance_3 IL_80494.2_IL_3B5F_001_C4_G11 | C | A | G | U | C | C | G | A | G | A | A | G | ||||||||||||||||||||
| IL_80494.2_Sequence_3 IL_80494.2_IL_3B5F_001_C4_G11 | C | A | G | U | C | C | * | G | A | G | A | A | G | true | 83 | 0 | 0 | 3.08 |
1 2 s35 1 12 cWW 2 11 tWH 3 4 s35 3 10 s55 4 5 s35 4 9 tHS 5 6 s35 5 8 bif 6 7 cWW 7 8 s35 8 9 s35 10 11 s35 11 12 s35 9 3 6BPhJAR3D SCFG/MRF model for IL_80494.2:
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 [12] // Initial node G116 - C138 from junction BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.009987650,0.018214897,0.011593253,0.190884602,0.000000000],[0.019392976,0.008431163,0.230141683,0.013571804,0.000000000],[0.011642323,0.218263837,0.002128924,0.024805687,0.000000000],[0.191253546,0.013354078,0.026056620,0.010276957,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Right Letter Distribution [0.375000000,0.375000000,0.125000000,0.125000000,0.000000000] | Left Index [1] | Right Index [12] // Basepair G116 - C138 cWW BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.074666681,0.002371906,0.132889684,0.002371906,0.000000000],[0.256608086,0.011223810,0.219910394,0.002371906,0.000000000],[0.002371906,0.002371906,0.016201685,0.024496808,0.000000000],[0.023560072,0.002371906,0.011353789,0.214857553,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [11] // Basepair C117 - A136 tWH FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.100000000,0.300000000,0.100000000,0.000000000] | Position [1] | Left Index [3] | Right Index [10] // Fixed node on left InitialNode | Left Length Distribution [0.993970181,0.005999820,0.000029999] | 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 [10] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [4] | Right Index [10] // Fixed node on right InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | 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 BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.033030289,0.033218255,0.270737673,0.156541726,0.000000000],[0.049633289,0.032263812,0.002877357,0.129470953,0.000000000],[0.000559599,0.000559599,0.016727646,0.001599435,0.000000000],[0.002956685,0.000559599,0.267664647,0.001599435,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // Basepair A119 - U134 tHS BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.019151570,0.404305861,0.005214221,0.005214221,0.000000000],[0.076986253,0.405940340,0.005214221,0.005214221,0.000000000],[0.005214221,0.005214221,0.018305611,0.005214221,0.000000000],[0.005214221,0.005214221,0.023168158,0.005214221,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // Basepair A120 - C133 bif BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009685694,0.019182219,0.010986155,0.195803621,0.000000000],[0.020623118,0.008749922,0.213456437,0.012400460,0.000000000],[0.010991697,0.213086471,0.002130191,0.024759915,0.000000000],[0.208179451,0.012376361,0.026149698,0.011438589,0.000000000],[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 [6] | Right Index [7] // Basepair G121 - C132 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 IL_80494.2:
> IL_80494.2 IL_3P49_012 G 116 C 138 GCAAAG*CCUAAAC > IL_80494.2 IL_1S72_057 C 1578 G 1618 CCAACU*ACGAACG > IL_80494.2 IL_3B5F_001 C 4 G 11 CAGUCC*GAGAAG