Alignment of HL_70782.2 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
2
I

6
2

3
7
1
I


In
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Alignment
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HL_70782.2_Instance_1 HL_70782.2,HL_8CRE_021,C954_G959CCUCAG
HL_70782.2_Sequence_1 HL_70782.28CRE_C954_G959CCUCAGtrue94000.56
HL_70782.2_Instance_2 HL_70782.2,HL_8P9A_134,C958_G963CCUCAG
HL_70782.2_Sequence_2 HL_70782.28P9A_C958_G963CCUCAGtrue94000.56
HL_70782.2_Instance_3 HL_70782.2,HL_4KR9_003,G10_C15GUGUCC
HL_70782.2_Sequence_3 HL_70782.24KR9_G10_C15GUGUCCtrue88001.12
HL_70782.2_Instance_4 HL_70782.2,HL_6FQL_001,U5_A9UUUAA
HL_70782.2_Sequence_4 HL_70782.26FQL_U5_A9UUUAAtrue100000.00

Conserved interactions between motif group positions in HL_70782.2:
1 3 cWW
JAR3D SCFG/MRF model for HL_70782.2:
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 [3] // Initial node
BasepairNode | Deletion Probability [0.0000000000110489] | Pair Probability [[0.009278367,0.017658581,0.010523925,0.194981980,0.000000000],[0.019540415,0.009513951,0.219788080,0.012727977,0.000000000],[0.010558860,0.208106937,0.002038293,0.023721161,0.000000000],[0.207216391,0.012440103,0.031948050,0.009956928,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.496627836,0.496627836,0.006437768,0.000306560] | Left Letter Distribution [0.125000000,0.125000000,0.125000000,0.625000000,0.000000000] | Right Length Distribution [0.003046923,0.246800731,0.252894576,0.490706886,0.006246191,0.000304692] | Right Letter Distribution [0.318181818,0.318181818,0.045454545,0.318181818,0.000000000] | Left Index [1] | Right Index [3] // Basepair C954 - G959 cWW 
HairpinNode  | Num Bases [1] | Left Index [2] | Right Index [2] | Norm Constant [1.000000000000000] // Hairpin node C955:C955
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.083333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.416666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.250000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.250000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C955
Sequences of instances from HL_70782.2:
> HL_70782.2  8CRE C  954 G  959
CCUCAG
> HL_70782.2  8P9A C  958 G  963
CCUCAG
> HL_70782.2  4KR9 G   10 C   15
GUGUCC
> HL_70782.2  6FQL U    5 A    9
UUUAA