| 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 3 3 | 7 3 I | 8 3 4 | 9 2 I | 10 2 5 | 11 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_66171.2_Instance_1 HL_66171.2_HL_4Y4O_142_C1612_G1619 | C | G | A | C | A | C | A | G | ||||||||
| HL_66171.2_Sequence_1 HL_66171.2_HL_4Y4O_142_C_1612_G_1619 | C | G | A | C | A | C | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_66171.2_Instance_2 HL_66171.2_HL_7A0S_040_C1628_G1635 | C | G | A | C | A | C | A | G | ||||||||
| HL_66171.2_Sequence_2 HL_66171.2_HL_7A0S_040_C_1628_G_1635 | C | G | A | C | A | C | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_66171.2_Instance_3 HL_66171.2_HL_4WF9_038_C1656_G1663 | C | G | A | C | A | C | A | G | ||||||||
| HL_66171.2_Sequence_3 HL_66171.2_HL_4WF9_038_C_1656_G_1663 | C | G | A | C | A | C | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_66171.2_Instance_4 HL_66171.2_HL_4V9F_042_C1687_G1694 | C | G | A | C | A | C | A | G | ||||||||
| HL_66171.2_Sequence_4 HL_66171.2_HL_4V9F_042_C_1687_G_1694 | C | G | A | C | A | C | A | G | true | 100 | 0 | 0 | 0.00 | |||
| HL_66171.2_Instance_5 HL_66171.2_HL_5TBW_041_C1844_G1851 | C | G | C | A | G | C | A | G | ||||||||
| HL_66171.2_Sequence_5 HL_66171.2_HL_5TBW_041_C_1844_G_1851 | C | G | C | A | G | C | A | G | true | 78 | 0 | 0 | 3.30 |
1 2 s35 1 5 cWW 2 4 s33 2 5 s55 3 4 s35 4 3 7BPh 2 4 6BRJAR3D SCFG/MRF model for HL_66171.2:
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 [5] // Initial node C1612 - G1619 from junction BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [1] | Right Index [5] // Basepair C1612 - G1619 cWW HairpinNode | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G1613:C1617 Interaction | Interacting Bases [1,1] | Pair Probability [[0.018518519,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.018518519,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.944444444,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.018518519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1613 Interaction | Interacting Bases [2,2] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.642857143,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.071428571,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1615 Interaction | Interacting Bases [3,3] | Pair Probability [[0.013513514,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.959459459,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1617 Insertion | Location [1] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.642857143,0.214285714,0.071428571,0.071428571,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1 Insertion | Location [2] | Length Distribution [0.009799118,0.979911808,0.009799118,0.000489956] | Letter Distribution [0.642857143,0.071428571,0.214285714,0.071428571,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2Sequences of instances from HL_66171.2:
> HL_66171.2 HL_4Y4O_142 C 1612 G 1619 CGACACAG > HL_66171.2 HL_7A0S_040 C 1628 G 1635 CGACACAG > HL_66171.2 HL_4WF9_038 C 1656 G 1663 CGACACAG > HL_66171.2 HL_4V9F_042 C 1687 G 1694 CGACACAG > HL_66171.2 HL_5TBW_041 C 1844 G 1851 CGCAGCAG