Alignment of HL_01472.3 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
5

2
5
5
I

6
6

3
7
5
I

8
5

4
9
4
I

10
3

5
11
2
I

12
2

6
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_01472.3_Instance_1 HL_01472.3_HL_5J7L_025_G1134_C1140GUCCGGC
HL_01472.3_Sequence_1 HL_01472.3_HL_5J7L_025_G_1134_C_1140GUCCGGCtrue96000.51
HL_01472.3_Instance_2 HL_01472.3_HL_4LFB_026_G1134_C1140GUUCGGC
HL_01472.3_Sequence_2 HL_01472.3_HL_4LFB_026_G_1134_C_1140GUUCGGCtrue100000.00
HL_01472.3_Instance_3 HL_01472.3_HL_4V9F_005_C136_G142CUUCGCG
HL_01472.3_Sequence_3 HL_01472.3_HL_4V9F_005_C136_G142CUUCGCGtrue96000.56

Conserved interactions between motif group positions in HL_01472.3:
1 2 s35 
1 6 cWW 
2 4 tSW 
4 6 s55 
5 6 s53 
JAR3D SCFG/MRF model for HL_01472.3:
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 [6] // Initial node G1134 - C1140 from junction 
BasepairNode | Deletion Probability [0.0000234451146992] | 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair G1134 - C1140 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.100000000,0.300000000,0.500000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [5] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001200211660] | Pair Probability [[0.027052754,0.025055635,0.003925724,0.184473855,0.000000000],[0.026633785,0.018016316,0.003925724,0.027753033,0.000000000],[0.030889124,0.003925724,0.003925724,0.019034091,0.000000000],[0.019470715,0.018890081,0.421698575,0.165329141,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.016116035,0.966962127,0.016116035,0.000805802] | Left Letter Distribution [0.100000000,0.300000000,0.100000000,0.500000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [4] // Basepair U1135 - G1138 tSW 
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node C1137:C1137
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.700000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[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 C1137
Sequences of instances from HL_01472.3:
> HL_01472.3 HL_5J7L_025 G 1134 C 1140
GUCCGGC
> HL_01472.3 HL_4LFB_026 G 1134 C 1140
GUUCGGC
> HL_01472.3 HL_4V9F_005 C  136 G  142
CUUCGCG