| 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 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_44781.1_Instance_1 HL_44781.1_HL_3D2V_001_G17_C22 | G | U | U | C | A | C | ||||||||||
| HL_44781.1_Sequence_1 HL_44781.1_HL_3D2V_001_G17_C22 | G | U | U | C | A | C | true | 100 | 0 | 0 | 0.00 | |||||
| HL_44781.1_Instance_2 HL_44781.1_HL_4Y4O_106_G139_C142A | G | G | G | A | A | C | ||||||||||
| HL_44781.1_Sequence_2 HL_44781.1_HL_4Y4O_106_G139_C_142A | G | G | G | A | A | C | true | 90 | 0 | 0 | 0.97 |
1 2 s33 1 5 cWW 2 3 s53 2 4 cWH 2 5 s35 3 4 s35 4 5 s35 5 4 7BPhJAR3D SCFG/MRF model for HL_44781.1:
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 G17 - C22 from junction BasepairNode | Deletion Probability [0.0000001182498160] | Pair Probability [[0.003823887,0.055746509,0.004354386,0.079088977,0.000000000],[0.006716761,0.026247934,0.079759134,0.005218628,0.000000000],[0.004306029,0.594150318,0.000820775,0.010514714,0.000000000],[0.078076789,0.037915021,0.009216620,0.004043518,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.023781213,0.951248514,0.023781213,0.001189061] | Left Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G17 - C22 cWW BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.002789345,0.002789345,0.012020284,0.012076678,0.000000000],[0.002789345,0.013413702,0.002789345,0.264197884,0.000000000],[0.109206963,0.002789345,0.009640600,0.002789345,0.000000000],[0.288738394,0.002789345,0.258095325,0.013084758,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair U19 - A21 cWH HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C20:C20 Interaction | Interacting Bases [1,1] | Pair Probability [[0.375000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.375000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C20Sequences of instances from HL_44781.1:
> HL_44781.1 HL_3D2V_001 G 17 C 22 GUUCAC > HL_44781.1 HL_4Y4O_106 G 139 C 142A GGGAAC