| 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 5 3 | 7 6 I | 8 7 4 | 9 8 I | 10 12 I | 11 13 5 | 12 13 I | 13 13 6 | 14 13 I | 15 13 7 | 16 12 I | 17 11 8 | 18 10 I | 19 9 9 | 20 2 I | 21 2 10 | 22 1 I | In acceptance region | Cutoff score | Full edit distance | Interior edit distance | Alignment score deficit |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| HL_99402.3_Instance_1 HL_99402.3_HL_7A0S_001_C58_G67 | C | G | A | U | U | A | C | C | U | G | |||||||||||||||||
| HL_99402.3_Sequence_1 HL_99402.3_HL_7A0S_001_C58_G67 | C | G | A | U | U | A | C | C | U | G | true | 100 | 0 | 0 | 0.00 | ||||||||||||
| HL_99402.3_Instance_2 HL_99402.3_HL_4V9F_001_U55_G64 | U | G | C | C | A | A | G | C | U | G | |||||||||||||||||
| HL_99402.3_Sequence_2 HL_99402.3_HL_4V9F_001_U55_G64 | U | G | C | C | A | A | G | C | U | G | true | 93 | 0 | 0 | 1.29 | ||||||||||||
| HL_99402.3_Instance_3 HL_99402.3_HL_4Y4O_103_U59_G68 | U | G | G | C | U | A | C | C | U | G | |||||||||||||||||
| HL_99402.3_Sequence_3 HL_99402.3_HL_4Y4O_103_U59_G68 | U | G | G | C | U | A | C | C | U | G | true | 95 | 0 | 0 | 0.99 | ||||||||||||
| HL_99402.3_Instance_4 HL_99402.3_HL_2XDB_001_U4_A13 | U | G | A | U | U | U | G | C | U | A | |||||||||||||||||
| HL_99402.3_Sequence_4 HL_99402.3_HL_2XDB_001_U4_A13 | U | G | A | U | U | U | G | C | U | A | true | 96 | 0 | 0 | 0.67 | ||||||||||||
| HL_99402.3_Instance_5 HL_99402.3_HL_2XD0_006_U4_A13 | U | G | A | U | U | U | G | C | U | A | |||||||||||||||||
| HL_99402.3_Sequence_5 HL_99402.3_HL_2XD0_006_U4_A13 | U | G | A | U | U | U | G | C | U | A | true | 96 | 0 | 0 | 0.67 |
1 10 cWW 2 5 s33 3 4 s35 5 6 cSH 5 7 cSH 6 7 s35 7 8 s35 8 9 s35 9 10 s35 5 2 7BRJAR3D SCFG/MRF model for HL_99402.3:
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 C58 - G67 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009733237,0.015573717,0.011528689,0.129390568,0.000000000],[0.130062747,0.016568213,0.143123808,0.013201463,0.000000000],[0.011681576,0.129441827,0.002485021,0.019215890,0.000000000],[0.171096022,0.012316634,0.173425084,0.011155504,0.000000000],[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 C58 - G67 cWW FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.214285714,0.214285714,0.071428571,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.357142857,0.071428571,0.500000000,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left InitialNode | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | Position [2] | Left Index [5] | Right Index [9] // 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 [5] | Right Index [8] // New Initial node after Fixed node FixedNode | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [5] | Right Index [8] // Fixed node on right 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 [5] | Right Index [7] // New Initial node after Fixed node HairpinNode | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [0.381499453226501] // Hairpin node U62:C64 Interaction | Interacting Bases [1,2] | Pair Probability [[0.109342186,0.092826534,0.004766805,0.027833881,0.000000000],[0.042129311,0.043253920,0.000483888,0.020439090,0.000000000],[0.020178040,0.000483888,0.040571218,0.042404139,0.000000000],[0.207785485,0.154312872,0.001857507,0.191331237,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U62 - A63 cSH Interaction | Interacting Bases [1,3] | Pair Probability [[0.035831964,0.038458679,0.244702065,0.045671713,0.000000000],[0.028039444,0.028645287,0.000766058,0.005534633,0.000000000],[0.006054028,0.000766058,0.030015390,0.026547693,0.000000000],[0.131063903,0.172895117,0.080539105,0.124468863,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U62 - C64 cSHSequences of instances from HL_99402.3:
> HL_99402.3 HL_7A0S_001 C 58 G 67 CGAUUACCUG > HL_99402.3 HL_4V9F_001 U 55 G 64 UGCCAAGCUG > HL_99402.3 HL_4Y4O_103 U 59 G 68 UGGCUACCUG > HL_99402.3 HL_2XDB_001 U 4 A 13 UGAUUUGCUA > HL_99402.3 HL_2XD0_006 U 4 A 13 UGAUUUGCUA