Alignment of HL_23481.4 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
4

3
7
4
I

8
4

4
9
4
I

10
4

5
11
3
I

12
3

6
13
2
I

14
2

7
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_23481.4_Instance_1 HL_23481.4_HL_4Y4O_108_G194_C201GAAACAUC
HL_23481.4_Sequence_1 HL_23481.4_HL_4Y4O_108_G194_C201GAAACAUCtrue100000.00
HL_23481.4_Instance_2 HL_23481.4_HL_5J7L_139_G194_C201GAAACAUC
HL_23481.4_Sequence_2 HL_23481.4_HL_5J7L_139_G194_C201GAAACAUCtrue100000.00
HL_23481.4_Instance_3 HL_23481.4_HL_7A0S_006_G171_C178GAAACAUC
HL_23481.4_Sequence_3 HL_23481.4_HL_7A0S_006_G171_C178GAAACAUCtrue100000.00
HL_23481.4_Instance_4 HL_23481.4_HL_4WF9_006_G197_C204GAAACAUC
HL_23481.4_Sequence_4 HL_23481.4_HL_4WF9_006_G197_C204GAAACAUCtrue100000.00
HL_23481.4_Instance_5 HL_23481.4_HL_4V9F_006_G164_C171GAAACAUC
HL_23481.4_Sequence_5 HL_23481.4_HL_4V9F_006_G164_C171GAAACAUCtrue100000.00
HL_23481.4_Instance_6 HL_23481.4_HL_5TBW_001_U38_A45UAAGCAUA
HL_23481.4_Sequence_6 HL_23481.4_HL_5TBW_001_U38_A45UAAGCAUAtrue76003.16
HL_23481.4_Instance_7 HL_23481.4_HL_3DIL_003_G124_C130GGAAUAC
HL_23481.4_Sequence_7 HL_23481.4_HL_3DIL_003_G124_C130GGAAUACtrue45007.28

Conserved interactions between motif group positions in HL_23481.4:
1 2 s35 
1 7 cWW 
2 4 s33 
2 6 tSH 
3 4 s35 
4 5 perp 
6 7 s35 
4 3 7BPh
2 4 7BPh
2 5 6BPh
7 6 7BPh
JAR3D SCFG/MRF model for HL_23481.4:
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 [7] // Initial node G194 - C201 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.004354767,0.047939157,0.004907494,0.091358094,0.000000000],[0.008490175,0.022785803,0.091995623,0.005768198,0.000000000],[0.004870614,0.552009327,0.000949036,0.011730113,0.000000000],[0.100980433,0.032392788,0.014788539,0.004679839,0.000000000],[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 [7] // Basepair G194 - C201 cWW 
BasepairNode | Deletion Probability [0.0000002600501426] | Pair Probability [[0.048876728,0.035529728,0.007110834,0.760351247,0.000000000],[0.006709565,0.006883088,0.000215097,0.000215097,0.000000000],[0.060028161,0.000643714,0.015410861,0.043314483,0.000000000],[0.007349450,0.006931752,0.000215097,0.000215097,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.146977400,0.846630090,0.006090502,0.000302008] | Left Letter Distribution [0.812500000,0.062500000,0.062500000,0.062500000,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [6] // Basepair A195 - U200 tSH 
HairpinNode  | Num Bases [3] | Left Index [3] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node A197:A199
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A197
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.147058824,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.833333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.009803922,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.009803922,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C198
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.722222222,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A199
Sequences of instances from HL_23481.4:
> HL_23481.4 HL_4Y4O_108 G  194 C  201
GAAACAUC
> HL_23481.4 HL_5J7L_139 G  194 C  201
GAAACAUC
> HL_23481.4 HL_7A0S_006 G  171 C  178
GAAACAUC
> HL_23481.4 HL_4WF9_006 G  197 C  204
GAAACAUC
> HL_23481.4 HL_4V9F_006 G  164 C  171
GAAACAUC
> HL_23481.4 HL_5TBW_001 U   38 A   45
UAAGCAUA
> HL_23481.4 HL_3DIL_003 G  124 C  130
GGAAUAC