Alignment of HL_27670.2 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
3
I

10
3

5
11
2
I

12
2

6
13
1
I


In
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Full
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Alignment
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HL_27670.2_Instance_1 HL_27670.2,HL_5J7L_144,G327_C335GUGACAGCC
HL_27670.2_Sequence_1 HL_27670.25J7L_G327_C335GUGACAGCCtrue77002.99
HL_27670.2_Instance_2 HL_27670.2,HL_4V9F_012,G334_C342GUGACAACC
HL_27670.2_Sequence_2 HL_27670.24V9F_G334_C342GUGACAACCtrue73003.50
HL_27670.2_Instance_3 HL_27670.2,HL_9DFE_011,G327_C335GUGAAAGCC
HL_27670.2_Sequence_3 HL_27670.29DFE_G327_C335GUGAAAGCCtrue91001.16
HL_27670.2_Instance_4 HL_27670.2,HL_4WF9_012,G370_C378GUAAUAAUC
HL_27670.2_Sequence_4 HL_27670.24WF9_G370_C378GUAAUAAUCtrue92001.00
HL_27670.2_Instance_5 HL_27670.2,HL_8P9A_119,G216_C224GUGAGAAUC
HL_27670.2_Sequence_5 HL_27670.28P9A_G216_C224GUGAGAAUCtrue93000.88
HL_27670.2_Instance_6 HL_27670.2,HL_8CRE_007,G215_C223GUGAGAAUC
HL_27670.2_Sequence_6 HL_27670.28CRE_G215_C223GUGAGAAUCtrue93000.88
HL_27670.2_Instance_7 HL_27670.2,HL_6DN2_002,G36_C43GUAUAGUC
HL_27670.2_Sequence_7 HL_27670.26DN2_G36_C43GUAUAGUCtrue97000.43
HL_27670.2_Instance_8 HL_27670.2,HL_4FRN_007,G56_C64GUUAUACUC
HL_27670.2_Sequence_8 HL_27670.24FRN_G56_C64GUUAUACUCtrue82002.32
HL_27670.2_Instance_9 HL_27670.2,HL_3F2X_002,G36_C43GUAUAGUC
HL_27670.2_Sequence_9 HL_27670.23F2X_G36_C43GUAUAGUCtrue97000.43
HL_27670.2_Instance_10 HL_27670.2,HL_4FRG_003,G58_C66GUUAUACUC
HL_27670.2_Sequence_10 HL_27670.24FRG_G58_C66GUUAUACUCtrue82002.32
HL_27670.2_Instance_11 HL_27670.2,HL_6DN2_004,G88_C95GUAGAGUC
HL_27670.2_Sequence_11 HL_27670.26DN2_G88_C95GUAGAGUCtrue100000.00
HL_27670.2_Instance_12 HL_27670.2,HL_3F2X_005,G88_C95GUAGAGUC
HL_27670.2_Sequence_12 HL_27670.23F2X_G88_C95GUAGAGUCtrue100000.00
HL_27670.2_Instance_13 HL_27670.2,HL_7A0S_012,G338_C346GUGAGAGUC
HL_27670.2_Sequence_13 HL_27670.27A0S_G338_C346GUGAGAGUCtrue97000.36

Conserved interactions between motif group positions in HL_27670.2:
1 2 s35 
1 6 cWW 
2 3 tWH 
3 6 s35 
4 5 s35 
6 5 7BPh
JAR3D SCFG/MRF model for HL_27670.2:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.003451650,0.050319857,0.003930508,0.071390050,0.000000000],[0.006062917,0.023692826,0.071994971,0.004710620,0.000000000],[0.003886858,0.633657809,0.000740877,0.009491158,0.000000000],[0.070476394,0.034224179,0.008319427,0.003649901,0.000000000],[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 [6] // Basepair G327 - C335 cWW 
HairpinNode  | Num Bases [4] | Left Index [2] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node U328:C334
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.016807828,0.003719599,0.017457680,0.003719599,0.000000000],[0.037405471,0.299728614,0.003719599,0.003719599,0.000000000],[0.003719599,0.008916125,0.028287238,0.016543496,0.000000000],[0.494317850,0.003719599,0.021580668,0.036637434,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U328 - A332 tWH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.300000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.500000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.033333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G333
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.033333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.233333333,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.033333333,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.700000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C334
Insertion    | Location [1] | Length Distribution [0.000000000,0.001174174,0.307927143,0.688065989,0.002700600,0.000132095] | Letter Distribution [0.418918919,0.067567568,0.310810811,0.202702703,0.000000000]// Insertion in Hairpin after nucleotide 2, position 1
Sequences of instances from HL_27670.2:
> HL_27670.2  5J7L G  327 C  335
GUGACAGCC
> HL_27670.2  4V9F G  334 C  342
GUGACAACC
> HL_27670.2  9DFE G  327 C  335
GUGAAAGCC
> HL_27670.2  4WF9 G  370 C  378
GUAAUAAUC
> HL_27670.2  8P9A G  216 C  224
GUGAGAAUC
> HL_27670.2  8CRE G  215 C  223
GUGAGAAUC
> HL_27670.2  6DN2 G   36 C   43
GUAUAGUC
> HL_27670.2  4FRN G   56 C   64
GUUAUACUC
> HL_27670.2  3F2X G   36 C   43
GUAUAGUC
> HL_27670.2  4FRG G   58 C   66
GUUAUACUC
> HL_27670.2  6DN2 G   88 C   95
GUAGAGUC
> HL_27670.2  3F2X G   88 C   95
GUAGAGUC
> HL_27670.2  7A0S G  338 C  346
GUGAGAGUC