Alignment of HL_86870.2 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
3
I

8
3

4
9
2
I

10
2

5
11
1
I


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Alignment
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HL_86870.2_Instance_1 HL_86870.2,HL_8CRE_017,G759_C764GUGUUC
HL_86870.2_Sequence_1 HL_86870.28CRE_G759_C764GUGUUCtrue100000.00
HL_86870.2_Instance_2 HL_86870.2,HL_8P9A_130,G763_C768GUCUUC
HL_86870.2_Sequence_2 HL_86870.28P9A_G763_C768GUCUUCtrue100000.00
HL_86870.2_Instance_3 HL_86870.2,HL_2Y9H_005,A10_U17ACGCGUGU
HL_86870.2_Sequence_3 HL_86870.22Y9H_A10_U17ACGCGUGUtrue37006.01
HL_86870.2_Instance_4 HL_86870.2,HL_9C75_001,C20_G24CAAUG
HL_86870.2_Sequence_4 HL_86870.29C75_C20_G24CAAUGtrue87001.26

Conserved interactions between motif group positions in HL_86870.2:
1 2 s35 
1 5 cWW 
2 3 s35 
2 4 cWW 
3 4 s55 
4 5 s35
JAR3D SCFG/MRF model for HL_86870.2:
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 [5] // Initial node
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009387651,0.019530919,0.010554546,0.207129074,0.000000000],[0.017651286,0.009411146,0.208023701,0.012435536,0.000000000],[0.010519639,0.219702921,0.002037417,0.031926571,0.000000000],[0.194898105,0.012723078,0.023711475,0.010356935,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [5] // Basepair G759 - C764 cWW 
BasepairNode | Deletion Probability [0.0000000286873767] | Pair Probability [[0.013755485,0.252292367,0.012281328,0.074771788,0.000000000],[0.015203076,0.016392676,0.071656399,0.013482061,0.000000000],[0.012024814,0.018677519,0.003791263,0.048434101,0.000000000],[0.018738100,0.014601062,0.015540908,0.398357054,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.375000000,0.375000000,0.125000000,0.000000000] | Right Length Distribution [0.738007380,0.009225092,0.003536285,0.246002460,0.003075031,0.000153752] | Right Letter Distribution [0.100000000,0.300000000,0.300000000,0.300000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair U760 - U763 cWW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U762:U762
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.250000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.083333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.416666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U762
Sequences of instances from HL_86870.2:
> HL_86870.2  8CRE G  759 C  764
GUGUUC
> HL_86870.2  8P9A G  763 C  768
GUCUUC
> HL_86870.2  2Y9H A   10 U   17
ACGCGUGU
> HL_86870.2  9C75 C   20 G   24
CAAUG