Alignment of HL_57875.1 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
2
I

8
2

4
9
1
I


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HL_57875.1_Instance_1 HL_57875.1,HL_2A64_001,G31_C36GGUUUC
HL_57875.1_Sequence_1 HL_57875.12A64_G31_C36GGUUUCtrue100000.00
HL_57875.1_Instance_2 HL_57875.1,HL_6N5P_002,G58_C64GUGAAGC
HL_57875.1_Sequence_2 HL_57875.16N5P_G58_C64GUGAAGCtrue56004.16
HL_57875.1_Instance_3 HL_57875.1,HL_3NDB_001,U162_G167UGUAGG
HL_57875.1_Sequence_3 HL_57875.13NDB_U162_G167UGUAGGtrue87001.20
HL_57875.1_Instance_4 HL_57875.1,HL_8CRE_016,C729_G734CAUUAG
HL_57875.1_Sequence_4 HL_57875.18CRE_C729_G734CAUUAGtrue94000.57
HL_57875.1_Instance_5 HL_57875.1,HL_8UO6_003,A77_U83AAUUAUU
HL_57875.1_Sequence_5 HL_57875.18UO6_A77_U83AAUUAUUtrue83001.60

Conserved interactions between motif group positions in HL_57875.1:
1 2 s35 
1 4 cWW 
2 4 s55 
3 4 s35
JAR3D SCFG/MRF model for HL_57875.1:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009623561,0.018192814,0.011137155,0.173271816,0.000000000],[0.072765384,0.012887643,0.174967580,0.012968885,0.000000000],[0.011170223,0.185110847,0.002256748,0.028148569,0.000000000],[0.171179579,0.012933473,0.092546057,0.010839667,0.000000000],[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 [4] // Basepair G31 - C36 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node G32:U35
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.357142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.214285714,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G32
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.214285714,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.071428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.357142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.357142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U35
Insertion    | Location [1] | Length Distribution [0.000000000,0.005879471,0.591866732,0.397844194,0.004213621,0.000195982] | Letter Distribution [0.321428571,0.035714286,0.107142857,0.535714286,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_57875.1:
> HL_57875.1  2A64 G   31 C   36
GGUUUC
> HL_57875.1  6N5P G   58 C   64
GUGAAGC
> HL_57875.1  3NDB U  162 G  167
UGUAGG
> HL_57875.1  8CRE C  729 G  734
CAUUAG
> HL_57875.1  8UO6 A   77 U   83
AAUUAUU