| 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_16898.2_Instance_1 HL_16898.2_HL_5J7L_156_U779_G785 | U | G | A | A | A | G | G | |||||||||
| HL_16898.2_Sequence_1 HL_16898.2_HL_5J7L_156_U779_G785 | U | G | A | A | A | G | G | true | 90 | 0 | 0 | 0.96 | ||||
| HL_16898.2_Instance_2 HL_16898.2_HL_4V9F_025_U872_G878 | U | G | A | A | A | G | G | |||||||||
| HL_16898.2_Sequence_2 HL_16898.2_HL_4V9F_025_U872_G878 | U | G | A | A | A | G | G | true | 90 | 0 | 0 | 0.96 | ||||
| HL_16898.2_Instance_3 HL_16898.2_HL_4LGT_001_C2594_G2599 | C | G | U | G | A | G | ||||||||||
| HL_16898.2_Sequence_3 HL_16898.2_HL_4LGT_001_C_2594_G_2599 | C | G | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||
| HL_16898.2_Instance_4 HL_16898.2_HL_6VMY_004_C287_G293 | C | C | A | A | G | C | G | |||||||||
| HL_16898.2_Sequence_4 HL_16898.2_HL_6VMY_004_C287_G293 | C | C | A | A | G | C | G | true | 65 | 0 | 0 | 3.29 | ||||
| HL_16898.2_Instance_5 HL_16898.2_HL_3DH3_001_C2594_G2599 | C | G | U | G | A | G | ||||||||||
| HL_16898.2_Sequence_5 HL_16898.2_HL_3DH3_001_C_2594_G_2599 | C | G | U | G | A | G | true | 100 | 0 | 0 | 0.00 | |||||
| HL_16898.2_Instance_6 HL_16898.2_HL_3DH3_003_C2594_G2599 | C | G | U | G | A | G | ||||||||||
| HL_16898.2_Sequence_6 HL_16898.2_HL_3DH3_003_C_2594_G_2599 | C | G | U | G | A | G | true | 100 | 0 | 0 | 0.00 |
1 2 s35 1 5 cWW 2 3 s35 2 4 tSW 2 5 s55 4 5 s55JAR3D SCFG/MRF model for HL_16898.2:
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 U779 - G785 from junction BasepairNode | Deletion Probability [0.0000016853335170] | Pair Probability [[0.009725060,0.015456119,0.011612777,0.139481247,0.000000000],[0.110048040,0.015196140,0.185380856,0.013989850,0.000000000],[0.011792020,0.142181183,0.002401060,0.019759909,0.000000000],[0.156825235,0.013232153,0.142088180,0.010830171,0.000000000],[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 [0.497737557,0.497737557,0.004319210,0.000205677] | Right Letter Distribution [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair U779 - G785 cWW BasepairNode | Deletion Probability [0.0000001231336240] | Pair Probability [[0.155616705,0.154871150,0.001934200,0.009352669,0.000000000],[0.180998274,0.008528493,0.029866127,0.007732903,0.000000000],[0.240589762,0.001934200,0.001934200,0.006342891,0.000000000],[0.167385278,0.008405952,0.015219036,0.009288161,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.437500000,0.062500000,0.062500000,0.437500000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair G780 - A783 tSW HairpinNode | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node A782:A782 Interaction | Interacting Bases [1,1] | Pair Probability [[0.437500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.437500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A782Sequences of instances from HL_16898.2:
> HL_16898.2 HL_5J7L_156 U 779 G 785 UGAAAGG > HL_16898.2 HL_4V9F_025 U 872 G 878 UGAAAGG > HL_16898.2 HL_4LGT_001 C 2594 G 2599 CGUGAG > HL_16898.2 HL_6VMY_004 C 287 G 293 CCAAGCG > HL_16898.2 HL_3DH3_001 C 2594 G 2599 CGUGAG > HL_16898.2 HL_3DH3_003 C 2594 G 2599 CGUGAG