Alignment of HL_04259.3 sequences from 3D to the JAR3D model

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The correspondence between sequences from 3D structures and the motif group is shown in blue and the JAR3D alignment of the sequences to the motif group is shown in black. Occasionally the two disagree, in which case the JAR3D alignment is shown in red.
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
7

3
7
7
I

8
8

4
9
8
I

10
8

5
11
7
I

12
7

6
13
6
I

14
5

7
15
2
I

16
2

8
17
1
I


In
acceptance
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Cutoff
score
Full
edit
distance
Interior
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Alignment
score
deficit
HL_04259.3_Instance_1 HL_04259.3,HL_4WF9_053,C2382_G2389CCUACAAG
HL_04259.3_Sequence_1 HL_04259.34WF9_C_2382_G_2389CCUACAAGtrue100000.00
HL_04259.3_Instance_2 HL_04259.3,HL_9DFE_055,C2355_G2362CCUGCAAG
HL_04259.3_Sequence_2 HL_04259.39DFE_C_2355_G_2362CCUGCAAGtrue94000.59
HL_04259.3_Instance_3 HL_04259.3,HL_7A0S_056,C2334_G2341CUGACACG
HL_04259.3_Sequence_3 HL_04259.37A0S_C_2334_G_2341CUGACACGtrue90000.97
HL_04259.3_Instance_4 HL_04259.3,HL_8KAL_001,U31_A38UAGAAAUA
HL_04259.3_Sequence_4 HL_04259.38KAL_U31_A38UAGAAAUAtrue81001.76
HL_04259.3_Instance_5 HL_04259.3,HL_7QR8_003,U71_A78UUGAAAAA
HL_04259.3_Sequence_5 HL_04259.37QR8_U71_A78UUGAAAAAtrue98000.16
HL_04259.3_Instance_6 HL_04259.3,HL_3RG5_006,G31_C39GCUUCAAAC
HL_04259.3_Sequence_6 HL_04259.33RG5_G31_C39GCUUCAAACtrue65003.31
HL_04259.3_Instance_7 HL_04259.3,HL_3R9X_002,G1514_C1521GGGGAACC
HL_04259.3_Sequence_7 HL_04259.33R9X_G_1514_C_1521GGGGAACCtrue81001.84

Conserved interactions between motif group positions in HL_04259.3:
1 2 s35 
1 8 cWW 
2 3 s35 
2 8 s55 
3 6 tSH 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
5 3 7BR
JAR3D SCFG/MRF model for HL_04259.3:
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 [0.0000244705618206] | Pair Probability [[0.009007838,0.017286514,0.010197105,0.189517347,0.000000000],[0.018944503,0.009245539,0.222360729,0.012260390,0.000000000],[0.010219144,0.211524103,0.001979579,0.023154143,0.000000000],[0.210767234,0.012009199,0.031842604,0.009684028,0.000000000],[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 C2382 - G2389 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.388888889,0.166666667,0.277777778,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // Fixed node on left for 4WF9|1|X|C|2383
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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.277777778,0.055555556,0.166666667,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // Fixed node on right for 4WF9|1|X|A|2388
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 [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000111424121612] | Pair Probability [[0.101673911,0.103759358,0.001196535,0.005700392,0.000000000],[0.102334093,0.104406517,0.001196535,0.001196535,0.000000000],[0.176692928,0.001196535,0.006232373,0.101006767,0.000000000],[0.184848561,0.106165889,0.001196535,0.001196535,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.850913138,0.147720949,0.001315324,0.000050589] | Left Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | 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 U2384 - A2387 tSH 
HairpinNode  | Num Bases [2] | Left Index [4] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A2385:C2386
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A2385
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.554054054,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.418918919,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.013513514,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.013513514,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C2386
Sequences of instances from HL_04259.3:
> HL_04259.3  4WF9 C 2382 G 2389
CCUACAAG
> HL_04259.3  9DFE C 2355 G 2362
CCUGCAAG
> HL_04259.3  7A0S C 2334 G 2341
CUGACACG
> HL_04259.3  8KAL U   31 A   38
UAGAAAUA
> HL_04259.3  7QR8 U   71 A   78
UUGAAAAA
> HL_04259.3  3RG5 G   31 C   39
GCUUCAAAC
> HL_04259.3  3R9X G 1514 C 1521
GGGGAACC