Alignment of HL_55195.3 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
3

2
5
2
I

6
2

3
7
1
I


In
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Alignment
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HL_55195.3_Instance_1 HL_55195.3,HL_9DFE_023,U826_G831UUUAGG
HL_55195.3_Sequence_1 HL_55195.39DFE_U826_G831UUUAGGtrue100000.00
HL_55195.3_Instance_2 HL_55195.3,HL_5J7L_157,U826_G831UUUAGG
HL_55195.3_Sequence_2 HL_55195.35J7L_U826_G831UUUAGGtrue100000.00
HL_55195.3_Instance_3 HL_55195.3,HL_4WF9_025,U871_G876UUUAGG
HL_55195.3_Sequence_3 HL_55195.34WF9_U871_G876UUUAGGtrue100000.00
HL_55195.3_Instance_4 HL_55195.3,HL_7A0S_024,U839_G844UUGAGG
HL_55195.3_Sequence_4 HL_55195.37A0S_U839_G844UUGAGGtrue91000.89
HL_55195.3_Instance_5 HL_55195.3,HL_4V9F_026,U919_G924UCGAAG
HL_55195.3_Sequence_5 HL_55195.34V9F_U919_G924UCGAAGtrue61003.72
HL_55195.3_Instance_6 HL_55195.3,HL_8P9A_156,G2110_C2114GGUAC
HL_55195.3_Sequence_6 HL_55195.38P9A_G_2110_C_2114GGUACtrue63003.49

Conserved interactions between motif group positions in HL_55195.3:
1 3 cWW
JAR3D SCFG/MRF model for HL_55195.3:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000000073929] | Pair Probability [[0.010579201,0.014464698,0.013226652,0.062177295,0.000000000],[0.245343400,0.023944112,0.066524081,0.014988012,0.000000000],[0.013457556,0.072711565,0.002986229,0.016057819,0.000000000],[0.100990956,0.013982220,0.316048022,0.012518180,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.000000000,0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.035714286,0.107142857,0.250000000,0.607142857,0.000000000] | Right Length Distribution [0.170928484,0.821824149,0.006905511,0.000341857] | Right Letter Distribution [0.214285714,0.071428571,0.642857143,0.071428571,0.000000000] | Left Index [1] | Right Index [3] // Basepair U826 - G831 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node A829:A829
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.812500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A829
Sequences of instances from HL_55195.3:
> HL_55195.3  9DFE U  826 G  831
UUUAGG
> HL_55195.3  5J7L U  826 G  831
UUUAGG
> HL_55195.3  4WF9 U  871 G  876
UUUAGG
> HL_55195.3  7A0S U  839 G  844
UUGAGG
> HL_55195.3  4V9F U  919 G  924
UCGAAG
> HL_55195.3  8P9A G 2110 C 2114
GGUAC