Alignment of HL_12703.2 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
3

3
7
3
I

8
3

4
9
2
I

10
2

5
11
1
I


In
acceptance
region


Cutoff
score

Full
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distance

Interior
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Alignment
score
deficit
HL_12703.2_Instance_1 HL_12703.2_HL_1HMH_006_G101_C111GGCCC
HL_12703.2_Sequence_1 HL_12703.2_HL_1HMH_006_G101_C111GGCCCtrue100000.00
HL_12703.2_Instance_2 HL_12703.2_HL_1HMH_004_G101_C111GGCCC
HL_12703.2_Sequence_2 HL_12703.2_HL_1HMH_004_G101_C111GGCCCtrue100000.00
HL_12703.2_Instance_3 HL_12703.2_HL_6AAY_001_C37_G44CAUUUUGG
HL_12703.2_Sequence_3 HL_12703.2_HL_6AAY_001_C37_G44CAUUUUGGtrue52004.58

Conserved interactions between motif group positions in HL_12703.2:
1 2 s35 
1 5 cWW 
2 3 s35 
2 5 s55 
3 4 s35 
JAR3D SCFG/MRF model for HL_12703.2:
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 [5] // Initial node G101 - C111 from junction 
BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.009574124,0.019028436,0.010936653,0.198530575,0.000000000],[0.017980846,0.009507606,0.212727929,0.013322270,0.000000000],[0.010896029,0.224384255,0.002069153,0.025416337,0.000000000],[0.197680266,0.013488440,0.024325847,0.010131233,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.500000000,0.166666667,0.000000000] | Left Index [1] | Right Index [5] // Basepair G101 - C111 cWW 
HairpinNode  | Num Bases [3] | Left Index [2] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node G102:C104
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G102
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C103
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.500000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C104
Insertion    | Location [2] | Length Distribution [0.651642683,0.016291067,0.326364377,0.005430356,0.000271518] | Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000]// Insertion in Hairpin after nucleotide 3, position 2
Sequences of instances from HL_12703.2:
> HL_12703.2 HL_1HMH_006 G  101 C  111
GGCCC
> HL_12703.2 HL_1HMH_004 G  101 C  111
GGCCC
> HL_12703.2 HL_6AAY_001 C   37 G   44
CAUUUUGG