Alignment of HL_35677.3 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
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
3
I

16
3

8
17
2
I

18
2

9
19
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_35677.3_Instance_1 HL_35677.3,HL_2XDB_001,U4_A13UGAUUUGCUA
HL_35677.3_Sequence_1 HL_35677.32XDB_U4_A13UGAUUUGCUAtrue100000.00
HL_35677.3_Instance_2 HL_35677.3,HL_7D8O_001,U4_A13UGAUUUGCUA
HL_35677.3_Sequence_2 HL_35677.37D8O_U4_A13UGAUUUGCUAtrue100000.00
HL_35677.3_Instance_3 HL_35677.3,HL_2XD0_006,U4_A13UGAUUUGCUA
HL_35677.3_Sequence_3 HL_35677.32XD0_U4_A13UGAUUUGCUAtrue100000.00
HL_35677.3_Instance_4 HL_35677.3,HL_5J7L_134,U59_G68UGCUAAUCUG
HL_35677.3_Sequence_4 HL_35677.35J7L_U59_G68UGCUAAUCUGtrue72004.27
HL_35677.3_Instance_5 HL_35677.3,HL_6YML_001,C15_G24CGGCUUCCUG
HL_35677.3_Sequence_5 HL_35677.36YML_C15_G24CGGCUUCCUGtrue83002.64
HL_35677.3_Instance_6 HL_35677.3,HL_6YL5_005,C15_G24CGGCUUCCUG
HL_35677.3_Sequence_6 HL_35677.36YL5_C15_G24CGGCUUCCUGtrue83002.64
HL_35677.3_Instance_7 HL_35677.3,HL_2Z75_003,C78_G86CUUCCUGCG
HL_35677.3_Sequence_7 HL_35677.32Z75_C78_G86CUUCCUGCGtrue65005.32

Conserved interactions between motif group positions in HL_35677.3:
1 9 cWW 
2 4 s33 
3 4 s35 
4 5 cSH 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
4 2 7BR
JAR3D SCFG/MRF model for HL_35677.3:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009118567,0.016058856,0.010472128,0.166496431,0.000000000],[0.058489878,0.011791140,0.199656881,0.012329983,0.000000000],[0.010572891,0.167465965,0.002139162,0.021001005,0.000000000],[0.205559214,0.011665843,0.087079895,0.010102162,0.000000000],[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 [9] // Basepair U4 - A13 cWW 
HairpinNode  | Num Bases [7] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Hairpin node G5:U12
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.036056826,0.035594376,0.001941603,0.027050431,0.000000000],[0.035680840,0.069868449,0.000425290,0.088979593,0.000000000],[0.026439075,0.000425290,0.035784576,0.038979976,0.000000000],[0.194325515,0.175692658,0.002126452,0.230629049,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U8 - U9 cSH 
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.722222222,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G5
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.277777778,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U7
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.277777778,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.388888889,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.277777778,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G10
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.722222222,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[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 C11
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.722222222,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U12
Insertion    | Location [1] | Length Distribution [0.568485889,0.428131469,0.003231181,0.000151462] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Insertion    | Location [3] | Length Distribution [0.850913138,0.147720949,0.001315324,0.000050589] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000]// Insertion in Hairpin after nucleotide 4, position 3
Insertion    | Location [4] | Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4
Sequences of instances from HL_35677.3:
> HL_35677.3  2XDB U    4 A   13
UGAUUUGCUA
> HL_35677.3  7D8O U    4 A   13
UGAUUUGCUA
> HL_35677.3  2XD0 U    4 A   13
UGAUUUGCUA
> HL_35677.3  5J7L U   59 G   68
UGCUAAUCUG
> HL_35677.3  6YML C   15 G   24
CGGCUUCCUG
> HL_35677.3  6YL5 C   15 G   24
CGGCUUCCUG
> HL_35677.3  2Z75 C   78 G   86
CUUCCUGCG