| 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 5 2 | 5 5 I | 6 6 3 | 7 5 I | 8 5 4 | 9 4 I | 10 3 5 | 11 2 I | 12 2 6 | 13 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_01472.3_Instance_1 HL_01472.3_HL_5J7L_025_G1134_C1140 | G | U | C | C | G | G | C | |||||||||||
| HL_01472.3_Sequence_1 HL_01472.3_HL_5J7L_025_G_1134_C_1140 | G | U | C | C | G | G | C | true | 96 | 0 | 0 | 0.51 | ||||||
| HL_01472.3_Instance_2 HL_01472.3_HL_4LFB_026_G1134_C1140 | G | U | U | C | G | G | C | |||||||||||
| HL_01472.3_Sequence_2 HL_01472.3_HL_4LFB_026_G_1134_C_1140 | G | U | U | C | G | G | C | true | 100 | 0 | 0 | 0.00 | ||||||
| HL_01472.3_Instance_3 HL_01472.3_HL_4V9F_005_C136_G142 | C | U | U | C | G | C | G | |||||||||||
| HL_01472.3_Sequence_3 HL_01472.3_HL_4V9F_005_C136_G142 | C | U | U | C | G | C | G | true | 96 | 0 | 0 | 0.56 |
1 2 s35 1 6 cWW 2 4 tSW 4 6 s55 5 6 s53JAR3D SCFG/MRF model for HL_01472.3:
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 [6] // Initial node G1134 - C1140 from junction BasepairNode | Deletion Probability [0.0000234451146992] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[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 [1] | Right Index [6] // Basepair G1134 - C1140 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // 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 [2] | Right Index [4] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.027052754,0.025055635,0.003925724,0.184473855,0.000000000],[0.026633785,0.018016316,0.003925724,0.027753033,0.000000000],[0.030889124,0.003925724,0.003925724,0.019034091,0.000000000],[0.019470715,0.018890081,0.421698575,0.165329141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | 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 [4] // Basepair U1135 - G1138 tSW HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C1137:C1137 Interaction | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C1137Sequences of instances from HL_01472.3:
> HL_01472.3 HL_5J7L_025 G 1134 C 1140 GUCCGGC > HL_01472.3 HL_4LFB_026 G 1134 C 1140 GUUCGGC > HL_01472.3 HL_4V9F_005 C 136 G 142 CUUCGCG