| 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 4 I | 8 4 4 | 9 4 I | 10 4 5 | 11 4 I | 12 4 6 | 13 3 I | 14 3 7 | 15 2 I | 16 2 8 | 17 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_99769.3_Instance_1 HL_99769.3,HL_5E6M_001,G12_C23 | G | U | A | G | U | GGU | A | U | C | |||||||||||||
| HL_99769.3_Sequence_1 HL_99769.35E6M_G12_C23 | G | U | A | G | U | GGU | A | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_99769.3_Instance_2 HL_99769.3,HL_4QEI_001,G12_C23 | G | U | A | G | U | GGU | A | U | C | |||||||||||||
| HL_99769.3_Sequence_2 HL_99769.34QEI_G12_C23 | G | U | A | G | U | GGU | A | U | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_99769.3_Instance_3 HL_99769.3,HL_2D6F_004,G912_C923 | G | U | A | G | U | GGUA | A | U | C | |||||||||||||
| HL_99769.3_Sequence_3 HL_99769.32D6F_G912_C923 | G | U | A | G | U | GGUA | A | U | C | true | 84 | 0 | 0 | 2.86 | ||||||||
| HL_99769.3_Instance_4 HL_99769.3,HL_6ZDU_001,C1271_G1282 | C | C | C | G | A | AUU | G | U | G | G | ||||||||||||
| HL_99769.3_Sequence_4 HL_99769.36ZDU_C_1271_G_1282 | C | C | C | G | A | AUU | G | U | G | G | true | 66 | 0 | 0 | 6.23 | |||||||
| HL_99769.3_Instance_5 HL_99769.3,HL_7A0S_009,A254_U265 | A | A | C | G | C | UUGC | G | U | U | |||||||||||||
| HL_99769.3_Sequence_5 HL_99769.37A0S_A254_U265 | A | A | C | G | C | UUGC | G | U | U | true | 70 | 0 | 0 | 5.39 | ||||||||
| HL_99769.3_Instance_6 HL_99769.3,HL_4WF9_068,C280_G291 | C | A | A | G | C | UUG | C | U | U | G | ||||||||||||
| HL_99769.3_Sequence_6 HL_99769.34WF9_C280_G291 | C | A | A | G | C | UUG | C | U | U | G | true | 77 | 0 | 0 | 4.15 |
1 2 s35 1 8 cWW 2 3 s35 2 7 cWW 3 4 s35 3 7 s55 4 5 s35 7 8 s35JAR3D SCFG/MRF model for HL_99769.3:
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 [8] // Initial node BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.009230865,0.018768751,0.010439530,0.202793908,0.000000000],[0.017539421,0.009244200,0.214720240,0.012476095,0.000000000],[0.010416702,0.225503918,0.002002873,0.028938765,0.000000000],[0.191649217,0.012664154,0.023565488,0.010045871,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair G12 - C23 cWW BasepairNode | Deletion Probability [0.0000097596267952] | Pair Probability [[0.012283522,0.167547459,0.011736018,0.127003216,0.000000000],[0.016782726,0.014047079,0.097138183,0.013115594,0.000000000],[0.011592759,0.087283062,0.003186300,0.045216319,0.000000000],[0.086875146,0.013857256,0.019259330,0.273076031,0.000000000],[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 [0.826344012,0.171868555,0.001718686,0.000068747] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U13 - U22 cWW HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node A14:A21 Interaction | Interacting Bases [1,1] | Pair Probability [[0.562500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A14 Interaction | Interacting Bases [2,2] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.812500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15 Interaction | Interacting Bases [3,3] | Pair Probability [[0.187500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.312500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.437500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U16 Interaction | Interacting Bases [4,4] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A21 Insertion | Location [3] | Length Distribution [0.000000000,0.000000000,0.005462242,0.658200191,0.333196777,0.003004233,0.000136556] | Letter Distribution [0.113636364,0.068181818,0.386363636,0.431818182,0.000000000]// Insertion in Hairpin after nucleotide 5, position 3Sequences of instances from HL_99769.3:
> HL_99769.3 5E6M G 12 C 23 GUAGUGGUAUC > HL_99769.3 4QEI G 12 C 23 GUAGUGGUAUC > HL_99769.3 2D6F G 912 C 923 GUAGUGGUAAUC > HL_99769.3 6ZDU C 1271 G 1282 CCCGAAUUGUGG > HL_99769.3 7A0S A 254 U 265 AACGCUUGCGUU > HL_99769.3 4WF9 C 280 G 291 CAAGCUUGCUUG