| 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 8 3 | 7 8 I | 8 9 4 | 9 9 I | 10 9 5 | 11 8 I | 12 8 6 | 13 7 I | 14 6 7 | 15 5 I | 16 4 8 | 17 3 I | 18 3 9 | 19 2 I | 20 2 10 | 21 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_92304.3_Instance_1 HL_92304.3_HL_1MMS_001_C1064_G1074 | C | U | U | A | G | A | A | G | C | A | G | |||||||||||||||
| HL_92304.3_Sequence_1 HL_92304.3_HL_1MMS_001_C_1064_G_1074 | C | U | U | A | G | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_92304.3_Instance_2 HL_92304.3_HL_5D8H_001_C1174_G1184 | C | U | U | A | G | A | A | G | C | A | G | |||||||||||||||
| HL_92304.3_Sequence_2 HL_92304.3_HL_5D8H_001_C_1174_G_1184 | C | U | U | A | G | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_92304.3_Instance_3 HL_92304.3_HL_6PRV_001_C1064_G1074 | C | U | U | A | G | A | A | G | C | A | G | |||||||||||||||
| HL_92304.3_Sequence_3 HL_92304.3_HL_6PRV_001_C_1064_G_1074 | C | U | U | A | G | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_92304.3_Instance_4 HL_92304.3_HL_5J7L_161_C1064_G1074 | C | U | U | A | G | A | A | G | C | A | G | |||||||||||||||
| HL_92304.3_Sequence_4 HL_92304.3_HL_5J7L_161_C_1064_G_1074 | C | U | U | A | G | A | A | G | C | A | G | true | 100 | 0 | 0 | 0.00 | ||||||||||
| HL_92304.3_Instance_5 HL_92304.3_HL_5TBW_027_C1239_G1249 | C | A | U | G | G | A | A | G | U | C | G | |||||||||||||||
| HL_92304.3_Sequence_5 HL_92304.3_HL_5TBW_027_C_1239_G_1249 | C | A | U | G | G | A | A | G | U | C | G | true | 76 | 0 | 0 | 4.90 |
1 2 s35 1 10 cWW 2 3 s35 2 9 cSW 2 10 s55 3 5 ---- 3 6 tSH 4 5 s35 5 6 s35 6 9 s35 7 8 s35 9 10 s35 3 6 6BPh 2 6 6BR 9 6 7BRJAR3D SCFG/MRF model for HL_92304.3:
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 [10] // Initial node C1064 - G1074 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009264105,0.016612765,0.010650229,0.193109658,0.000000000],[0.019697072,0.009435223,0.250623774,0.013396622,0.000000000],[0.010769834,0.197270651,0.002030047,0.022795742,0.000000000],[0.195613131,0.012907388,0.026006356,0.009817401,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [10] // Basepair C1064 - G1074 cWW BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.102656694,0.041237119,0.002830084,0.000819767,0.000000000],[0.098451458,0.001578518,0.000218513,0.000859783,0.000000000],[0.101257109,0.000218513,0.017639504,0.000687240,0.000000000],[0.614140626,0.007998128,0.005375012,0.004031932,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [9] // Basepair U1065 - A1073 cSW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.642857143,0.071428571,0.214285714,0.000000000] | Position [2] | Left Index [3] | Right Index [8] // 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [7] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Left Index [3] | Right Index [6] // New Initial node after Fixed node BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.044038328,0.040224777,0.000489063,0.002405801,0.000000000],[0.044208451,0.041595888,0.000489063,0.000489063,0.000000000],[0.045477317,0.000489063,0.003022650,0.040601316,0.000000000],[0.413191926,0.316430412,0.003423441,0.003423441,0.000000000],[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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair U1066 - A1069 tSH HairpinNode | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A1067:G1068 Interaction | Interacting Bases [1,1] | Pair Probability [[0.642857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.214285714,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1067 Interaction | Interacting Bases [2,2] | Pair Probability [[0.071428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.785714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.071428571,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G1068Sequences of instances from HL_92304.3:
> HL_92304.3 HL_1MMS_001 C 1064 G 1074 CUUAGAAGCAG > HL_92304.3 HL_5D8H_001 C 1174 G 1184 CUUAGAAGCAG > HL_92304.3 HL_6PRV_001 C 1064 G 1074 CUUAGAAGCAG > HL_92304.3 HL_5J7L_161 C 1064 G 1074 CUUAGAAGCAG > HL_92304.3 HL_5TBW_027 C 1239 G 1249 CAUGGAAGUCG