| 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 3 3 | 7 3 I | 8 3 4 | 9 3 I | 10 3 5 | 11 3 I | 12 3 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_46891.2_Instance_1 HL_46891.2_HL_3R4F_004_A51_U58 | A | U | G | G | U | U | G | U | ||||||||||||||
| HL_46891.2_Sequence_1 HL_46891.2_HL_3R4F_004_A51_U58 | A | U | G | G | U | U | G | U | true | 98 | 0 | 0 | 0.25 | |||||||||
| HL_46891.2_Instance_2 HL_46891.2_HL_3R4F_002_A51_U58 | A | U | G | G | U | U | G | U | ||||||||||||||
| HL_46891.2_Sequence_2 HL_46891.2_HL_3R4F_002_A51_U58 | A | U | G | G | U | U | G | U | true | 98 | 0 | 0 | 0.25 | |||||||||
| HL_46891.2_Instance_3 HL_46891.2_HL_4V9F_055_C2281_G2289 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_46891.2_Sequence_3 HL_46891.2_HL_4V9F_055_C_2281_G_2289 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_46891.2_Instance_4 HL_46891.2_HL_4WF9_049_C2275_G2283 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_46891.2_Sequence_4 HL_46891.2_HL_4WF9_049_C_2275_G_2283 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_46891.2_Instance_5 HL_46891.2_HL_7A0S_052_C2227_G2235 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_46891.2_Sequence_5 HL_46891.2_HL_7A0S_052_C_2227_G_2235 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_46891.2_Instance_6 HL_46891.2_HL_5TBW_054_C2616_G2624 | C | U | G | G | G | G | C | G | G | |||||||||||||
| HL_46891.2_Sequence_6 HL_46891.2_HL_5TBW_054_C_2616_G_2624 | C | U | G | G | G | G | C | G | G | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_46891.2_Instance_7 HL_46891.2_HL_4V84_034_U6185_G6192 | U | U | A | G | G | U | A | G | ||||||||||||||
| HL_46891.2_Sequence_7 HL_46891.2_HL_4V84_034_U_6185_G_6192 | U | U | A | G | G | U | A | G | true | 71 | 0 | 0 | 3.43 | |||||||||
| HL_46891.2_Instance_8 HL_46891.2_HL_6UFG_003_G69_C76 | G | G | U | U | G | G | C | C | ||||||||||||||
| HL_46891.2_Sequence_8 HL_46891.2_HL_6UFG_003_G69_C76 | G | G | U | U | G | G | C | C | true | 56 | 0 | 0 | 5.13 | |||||||||
| HL_46891.2_Instance_9 HL_46891.2_HL_6UFH_001_G13_C20 | G | C | G | A | U | C | A | C | ||||||||||||||
| HL_46891.2_Sequence_9 HL_46891.2_HL_6UFH_001_G13_C20 | G | C | G | A | U | C | A | C | true | 79 | 0 | 0 | 2.47 | |||||||||
| HL_46891.2_Instance_10 HL_46891.2_HL_6UFG_001_G13_C20 | G | C | G | A | U | C | A | C | ||||||||||||||
| HL_46891.2_Sequence_10 HL_46891.2_HL_6UFG_001_G13_C20 | G | C | G | A | U | C | A | C | true | 79 | 0 | 0 | 2.47 | |||||||||
| HL_46891.2_Instance_11 HL_46891.2_HL_6UFM_006_G80_C87 | G | G | U | G | A | G | C | C | ||||||||||||||
| HL_46891.2_Sequence_11 HL_46891.2_HL_6UFM_006_G80_C87 | G | G | U | G | A | G | C | C | true | 59 | 0 | 0 | 4.86 |
1 2 s35 1 8 cWW 3 4 s35 4 5 s35 5 6 s35 6 7 s35 7 8 s35JAR3D SCFG/MRF model for HL_46891.2:
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 [8] // Initial node A51 - U58 from junction BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008929643,0.017333964,0.010216417,0.188932372,0.000000000],[0.040688900,0.010370554,0.209686185,0.012117231,0.000000000],[0.010239314,0.209669489,0.002013651,0.026901358,0.000000000],[0.173649179,0.012115827,0.057257976,0.009877940,0.000000000],[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 [8] // Basepair A51 - U58 cWW HairpinNode | Num Bases [6] | Left Index [2] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node U52:G57 Interaction | Interacting Bases [1,1] | Pair Probability [[0.038461538,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.192307692,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.192307692,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.576923077,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U52 Interaction | Interacting Bases [2,2] | Pair Probability [[0.115384615,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.192307692,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G53 Interaction | Interacting Bases [3,3] | Pair Probability [[0.192307692,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.653846154,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.115384615,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G54 Interaction | Interacting Bases [4,4] | Pair Probability [[0.115384615,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.038461538,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.346153846,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U55 Interaction | Interacting Bases [5,5] | Pair Probability [[0.038461538,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.192307692,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.269230769,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U56 Interaction | Interacting Bases [6,6] | Pair Probability [[0.269230769,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.192307692,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.038461538,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G57 Insertion | Location [1] | Length Distribution [0.633943052,0.364188787,0.001786044,0.000082117] | Letter Distribution [0.083333333,0.083333333,0.750000000,0.083333333,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1Sequences of instances from HL_46891.2:
> HL_46891.2 HL_3R4F_004 A 51 U 58 AUGGUUGU > HL_46891.2 HL_3R4F_002 A 51 U 58 AUGGUUGU > HL_46891.2 HL_4V9F_055 C 2281 G 2289 CUGGGGCGG > HL_46891.2 HL_4WF9_049 C 2275 G 2283 CUGGGGCGG > HL_46891.2 HL_7A0S_052 C 2227 G 2235 CUGGGGCGG > HL_46891.2 HL_5TBW_054 C 2616 G 2624 CUGGGGCGG > HL_46891.2 HL_4V84_034 U 6185 G 6192 UUAGGUAG > HL_46891.2 HL_6UFG_003 G 69 C 76 GGUUGGCC > HL_46891.2 HL_6UFH_001 G 13 C 20 GCGAUCAC > HL_46891.2 HL_6UFG_001 G 13 C 20 GCGAUCAC > HL_46891.2 HL_6UFM_006 G 80 C 87 GGUGAGCC