| 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_84299.4_Instance_1 HL_84299.4,HL_8P9A_197,G330_C338 | G | A | U | A | G | U | G | G | C | |||||||||||||
| HL_84299.4_Sequence_1 HL_84299.48P9A_G330_C338 | G | A | U | A | G | U | G | G | C | true | 100 | 0 | 0 | 0.02 | ||||||||
| HL_84299.4_Instance_2 HL_84299.4,HL_8CRE_198,G328_C336 | G | A | U | A | G | U | G | G | C | |||||||||||||
| HL_84299.4_Sequence_2 HL_84299.48CRE_G328_C336 | G | A | U | A | G | U | G | G | C | true | 100 | 0 | 0 | 0.02 | ||||||||
| HL_84299.4_Instance_3 HL_84299.4,HL_4LFB_006,G259_C267 | G | G | U | A | A | U | G | G | C | |||||||||||||
| HL_84299.4_Sequence_3 HL_84299.44LFB_G259_C267 | G | G | U | A | A | U | G | G | C | true | 96 | 0 | 0 | 0.52 | ||||||||
| HL_84299.4_Instance_4 HL_84299.4,HL_5J7L_006,G259_C267 | G | G | U | A | A | C | G | G | C | |||||||||||||
| HL_84299.4_Sequence_4 HL_84299.45J7L_G259_C267 | G | G | U | A | A | C | G | G | C | true | 92 | 0 | 0 | 1.10 | ||||||||
| HL_84299.4_Instance_5 HL_84299.4,HL_4R4V_003,G689_C697 | G | U | U | G | A | C | U | A | C | |||||||||||||
| HL_84299.4_Sequence_5 HL_84299.44R4V_G689_C697 | G | U | U | G | A | C | U | A | C | true | 46 | 0 | 0 | 7.62 | ||||||||
| HL_84299.4_Instance_6 HL_84299.4,HL_5T83_003,G77_C85 | G | A | U | A | A | A | A | G | C | |||||||||||||
| HL_84299.4_Sequence_6 HL_84299.45T83_G77_C85 | G | A | U | A | A | A | A | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_84299.4_Instance_7 HL_84299.4,HL_7MLW_003,G112_C120 | G | A | U | A | A | A | A | G | C | |||||||||||||
| HL_84299.4_Sequence_7 HL_84299.47MLW_G112_C120 | G | A | U | A | A | A | A | G | C | true | 100 | 0 | 0 | 0.00 | ||||||||
| HL_84299.4_Instance_8 HL_84299.4,HL_6DLR_003,G82_C90 | G | A | U | A | G | A | A | G | C | |||||||||||||
| HL_84299.4_Sequence_8 HL_84299.46DLR_G82_C90 | G | A | U | A | G | A | A | G | C | true | 99 | 0 | 0 | 0.20 | ||||||||
| HL_84299.4_Instance_9 HL_84299.4,HL_2BH2_002,G1949_C1957 | G | G | U | A | A | G | U | U | C | |||||||||||||
| HL_84299.4_Sequence_9 HL_84299.42BH2_G_1949_C_1957 | G | G | U | A | A | G | U | U | C | true | 67 | 0 | 0 | 4.62 |
1 2 s35 1 8 cWW 2 3 s35 2 7 tWH 3 5 s33 4 5 s35 5 6 s35 6 7 s35 7 8 s35 3 6 6BPhJAR3D SCFG/MRF model for HL_84299.4:
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 [0.0000003956735078] | Pair Probability [[0.009108592,0.018969937,0.010372256,0.188391897,0.000000000],[0.015999490,0.008931890,0.189988229,0.012430900,0.000000000],[0.010257066,0.278079433,0.001955106,0.025046309,0.000000000],[0.185980842,0.012902074,0.021954217,0.009631760,0.000000000],[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 [0.224265942,0.771181521,0.004338660,0.000213878] | Right Letter Distribution [0.055555556,0.055555556,0.833333333,0.055555556,0.000000000] | Left Index [1] | Right Index [8] // Basepair G330 - C338 cWW BasepairNode | Deletion Probability [0.0000132986348294] | Pair Probability [[0.301754209,0.002857512,0.281952459,0.002857512,0.000000000],[0.044060119,0.012417181,0.002857512,0.002857512,0.000000000],[0.002857512,0.007453457,0.140191373,0.124724163,0.000000000],[0.039246899,0.002857512,0.013413100,0.017641969,0.000000000],[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 [0.883805084,0.115305590,0.000858659,0.000030666] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair A331 - G336 tWH HairpinNode | Num Bases [4] | Left Index [3] | Right Index [6] | Norm Constant [1.000000000000000] // Hairpin node U332:U335 Interaction | Interacting Bases [1,1] | Pair Probability [[0.007692308,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.007692308,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.007692308,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.976923077,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U332 Interaction | Interacting Bases [2,2] | Pair Probability [[0.772727273,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.136363636,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A333 Interaction | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.409090909,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G334 Interaction | Interacting Bases [4,4] | Pair Probability [[0.318181818,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.227272727,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.045454545,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.409090909,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U335 Insertion | Location [2] | Length Distribution [0.883805084,0.115305590,0.000858659,0.000030666] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 2Sequences of instances from HL_84299.4:
> HL_84299.4 8P9A G 330 C 338 GAUAGUGGC > HL_84299.4 8CRE G 328 C 336 GAUAGUGGC > HL_84299.4 4LFB G 259 C 267 GGUAAUGGC > HL_84299.4 5J7L G 259 C 267 GGUAACGGC > HL_84299.4 4R4V G 689 C 697 GUUGACUAC > HL_84299.4 5T83 G 77 C 85 GAUAAAAGC > HL_84299.4 7MLW G 112 C 120 GAUAAAAGC > HL_84299.4 6DLR G 82 C 90 GAUAGAAGC > HL_84299.4 2BH2 G 1949 C 1957 GGUAAGUUC