Alignment of HL_30068.2 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
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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Alignment
score
deficit
HL_30068.2_Instance_1 HL_30068.2,HL_8P9A_113,U38_A45UAAGCAUA
HL_30068.2_Sequence_1 HL_30068.28P9A_U38_A45UAAGCAUAtrue100000.00
HL_30068.2_Instance_2 HL_30068.2,HL_8CRE_001,U37_A44UAAGCAUA
HL_30068.2_Sequence_2 HL_30068.28CRE_U37_A44UAAGCAUAtrue100000.00
HL_30068.2_Instance_3 HL_30068.2,HL_4WF9_006,G197_C204GAAACAUC
HL_30068.2_Sequence_3 HL_30068.24WF9_G197_C204GAAACAUCtrue97000.30
HL_30068.2_Instance_4 HL_30068.2,HL_5J7L_139,G194_C201GAAACAUC
HL_30068.2_Sequence_4 HL_30068.25J7L_G194_C201GAAACAUCtrue97000.30
HL_30068.2_Instance_5 HL_30068.2,HL_4V9F_006,G164_C171GAAACAUC
HL_30068.2_Sequence_5 HL_30068.24V9F_G164_C171GAAACAUCtrue97000.30
HL_30068.2_Instance_6 HL_30068.2,HL_7A0S_006,G171_C178GAAACAUC
HL_30068.2_Sequence_6 HL_30068.27A0S_G171_C178GAAACAUCtrue97000.30
HL_30068.2_Instance_7 HL_30068.2,HL_9DFE_005,G194_C201GAAACAUC
HL_30068.2_Sequence_7 HL_30068.29DFE_G194_C201GAAACAUCtrue97000.30
HL_30068.2_Instance_8 HL_30068.2,HL_4WF9_058,C2578_G2584CUGUUCG
HL_30068.2_Sequence_8 HL_30068.24WF9_C_2578_G_2584CUGUUCGtrue98000.21
HL_30068.2_Instance_9 HL_30068.2,HL_5J7L_195,C2551_G2557CUGUUCG
HL_30068.2_Sequence_9 HL_30068.25J7L_C_2551_G_2557CUGUUCGtrue98000.21
HL_30068.2_Instance_10 HL_30068.2,HL_9DFE_060,C2551_G2557CUGUUCG
HL_30068.2_Sequence_10 HL_30068.29DFE_C_2551_G_2557CUGUUCGtrue98000.21
HL_30068.2_Instance_11 HL_30068.2,HL_8CRE_062,U2892_A2898UUGUUCA
HL_30068.2_Sequence_11 HL_30068.28CRE_U_2892_A_2898UUGUUCAtrue98000.21
HL_30068.2_Instance_12 HL_30068.2,HL_8P9A_174,U2920_A2926UUGUUCA
HL_30068.2_Sequence_12 HL_30068.28P9A_U_2920_A_2926UUGUUCAtrue98000.21
HL_30068.2_Instance_13 HL_30068.2,HL_7A0S_061,C2530_G2536CUGUUCG
HL_30068.2_Sequence_13 HL_30068.27A0S_C_2530_G_2536CUGUUCGtrue98000.21
HL_30068.2_Instance_14 HL_30068.2,HL_3DIL_003,G124_C130GGAAUAC
HL_30068.2_Sequence_14 HL_30068.23DIL_G124_C130GGAAUACtrue69002.90
HL_30068.2_Instance_15 HL_30068.2,HL_4V9F_073,U2586_G2592UUGUUCG
HL_30068.2_Sequence_15 HL_30068.24V9F_U_2586_G_2592UUGUUCGtrue84001.52

Conserved interactions between motif group positions in HL_30068.2:
1 2 s35 
1 6 cWW 
2 4 s33 
2 5 tSH 
3 4 s35 
5 6 s35
JAR3D SCFG/MRF model for HL_30068.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008510759,0.016213523,0.009713729,0.167081391,0.000000000],[0.033964789,0.009661767,0.205335034,0.011535183,0.000000000],[0.009722232,0.222518473,0.001914516,0.021364893,0.000000000],[0.206368725,0.011356031,0.055505862,0.009233092,0.000000000],[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 [6] // Basepair U38 - A45 cWW 
BasepairNode | Deletion Probability [0.0000000103657687] | Pair Probability [[0.058981802,0.044745470,0.002617483,0.272958464,0.000000000],[0.057336414,0.053616417,0.002617483,0.002617483,0.000000000],[0.065409088,0.002617483,0.191871936,0.037914146,0.000000000],[0.058546679,0.142914688,0.002617483,0.002617483,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.532198331,0.466088110,0.001636173,0.000077387] | Left Letter Distribution [0.833333333,0.055555556,0.055555556,0.055555556,0.000000000] | Right Length Distribution [0.003310710,0.993213044,0.003310710,0.000165536] | Right Letter Distribution [0.441176471,0.029411765,0.029411765,0.500000000,0.000000000] | Left Index [2] | Right Index [5] // Basepair A39 - U44 tSH 
HairpinNode  | Num Bases [2] | Left Index [3] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G41:C42
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.382352941,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.029411765,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.558823529,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.029411765,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G41
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.088235294,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.441176471,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.029411765,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.441176471,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C42
Sequences of instances from HL_30068.2:
> HL_30068.2  8P9A U   38 A   45
UAAGCAUA
> HL_30068.2  8CRE U   37 A   44
UAAGCAUA
> HL_30068.2  4WF9 G  197 C  204
GAAACAUC
> HL_30068.2  5J7L G  194 C  201
GAAACAUC
> HL_30068.2  4V9F G  164 C  171
GAAACAUC
> HL_30068.2  7A0S G  171 C  178
GAAACAUC
> HL_30068.2  9DFE G  194 C  201
GAAACAUC
> HL_30068.2  4WF9 C 2578 G 2584
CUGUUCG
> HL_30068.2  5J7L C 2551 G 2557
CUGUUCG
> HL_30068.2  9DFE C 2551 G 2557
CUGUUCG
> HL_30068.2  8CRE U 2892 A 2898
UUGUUCA
> HL_30068.2  8P9A U 2920 A 2926
UUGUUCA
> HL_30068.2  7A0S C 2530 G 2536
CUGUUCG
> HL_30068.2  3DIL G  124 C  130
GGAAUAC
> HL_30068.2  4V9F U 2586 G 2592
UUGUUCG