| 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 11 3 | 7 11 I | 8 12 4 | 9 11 I | 10 11 5 | 11 10 I | 12 9 6 | 13 8 I | 14 7 7 | 15 6 I | 16 5 8 | 17 2 I | 18 2 9 | 19 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_67079.1_Instance_1 HL_67079.1,HL_4V7M_040,G51_C61 | G | G | U | U | CG | A | A | U | C | C | ||||||||||||||
| HL_67079.1_Sequence_1 HL_67079.14V7M_G51_C61 | G | G | U | U | CG | A | A | U | C | C | true | 94 | 0 | 0 | 0.94 | |||||||||
| HL_67079.1_Instance_2 HL_67079.1,HL_4V9I_040,C52_G62 | C | A | A | C | UC | U | A | C | C | G | ||||||||||||||
| HL_67079.1_Sequence_2 HL_67079.14V9I_C52_G62 | C | A | A | C | UC | U | A | C | C | G | true | 80 | 0 | 0 | 3.19 | |||||||||
| HL_67079.1_Instance_3 HL_67079.1,HL_8P9A_222,A1550_U1561 | A | U | U | G | UA | A | U | U | A | U | U | |||||||||||||
| HL_67079.1_Sequence_3 HL_67079.18P9A_A_1550_U_1561 | A | U | U | G | UA | A | U | U | A | U | U | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_67079.1_Instance_4 HL_67079.1,HL_8CRE_223,A1537_U1548 | A | U | U | G | UA | A | U | U | G | U | U | |||||||||||||
| HL_67079.1_Sequence_4 HL_67079.18CRE_A_1537_U_1548 | A | U | U | G | UA | A | U | U | G | U | U | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 9 cWW 2 3 s35 2 9 s55 3 4 s35 3 5 tWH 4 5 s55 5 8 s33 6 7 s35 8 9 s55JAR3D SCFG/MRF model for HL_67079.1:
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 [9] // Initial node BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009277126,0.019957246,0.010267742,0.217429628,0.000000000],[0.017754432,0.009419825,0.205851134,0.011718309,0.000000000],[0.010258285,0.207085186,0.002025617,0.038411566,0.000000000],[0.194231032,0.012046506,0.023601563,0.010664802,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair G51 - C61 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.250000000,0.083333333,0.250000000,0.416666667,0.000000000] | Position [1] | Left Index [2] | Right Index [8] // Fixed node on left for 4V7M|1|AY|G|52 InitialNode | Left Length Distribution [0.995990040,0.003999960,0.000010000] | 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 [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.416666667,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // Fixed node on right for 4V7M|1|AY|A|58 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Right Letter Distribution [0.375000000,0.125000000,0.375000000,0.125000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.083333333,0.250000000,0.083333333,0.583333333,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right for 4V7M|1|AY|A|57 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.416666667,0.083333333,0.083333333,0.416666667,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // Fixed node on right for 4V7M|1|AY|G|56 InitialNode | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000000006078908] | Pair Probability [[0.017820521,0.003943710,0.018509527,0.044576464,0.000000000],[0.039659197,0.317787634,0.003943710,0.003943710,0.000000000],[0.003943710,0.009453333,0.029991579,0.017540263,0.000000000],[0.423217119,0.003943710,0.022880930,0.038844885,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Right Letter Distribution [0.250000000,0.250000000,0.150000000,0.350000000,0.000000000] | Left Index [3] | Right Index [5] // Basepair U53 - A57 tWH HairpinNode | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node U54:U54 Interaction | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.250000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.416666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U54Sequences of instances from HL_67079.1:
> HL_67079.1 4V7M G 51 C 61 GGUUCGAAUCC > HL_67079.1 4V9I C 52 G 62 CAACUCUACCG > HL_67079.1 8P9A A 1550 U 1561 AUUGUAAUUAUU > HL_67079.1 8CRE A 1537 U 1548 AUUGUAAUUGUU