Alignment of HL_15942.4 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


In
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Cutoff
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Full
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Interior
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Alignment
score
deficit
HL_15942.4_Instance_1 HL_15942.4_HL_5J7L_157_U826_G831UUUAGG
HL_15942.4_Sequence_1 HL_15942.4_HL_5J7L_157_U826_G831UUUAGGtrue100000.00
HL_15942.4_Instance_2 HL_15942.4_HL_4WF9_025_U871_G876UUUAGG
HL_15942.4_Sequence_2 HL_15942.4_HL_4WF9_025_U871_G876UUUAGGtrue100000.00
HL_15942.4_Instance_3 HL_15942.4_HL_4Y4O_127_U826_G831UUUAGG
HL_15942.4_Sequence_3 HL_15942.4_HL_4Y4O_127_U826_G831UUUAGGtrue100000.00
HL_15942.4_Instance_4 HL_15942.4_HL_5TBW_022_C958_G963CCUCAG
HL_15942.4_Sequence_4 HL_15942.4_HL_5TBW_022_C958_G963CCUCAGtrue59003.89
HL_15942.4_Instance_5 HL_15942.4_HL_4V9F_026_U919_G924UCGAAG
HL_15942.4_Sequence_5 HL_15942.4_HL_4V9F_026_U919_G924UCGAAGtrue81001.76
HL_15942.4_Instance_6 HL_15942.4_HL_7A0S_024_U839_G844UUGAGG
HL_15942.4_Sequence_6 HL_15942.4_HL_7A0S_024_U839_G844UUGAGGtrue94000.59

Conserved interactions between motif group positions in HL_15942.4:
1 2 perp 
1 4 cWW 
2 3 s35 
JAR3D SCFG/MRF model for HL_15942.4:
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 [4] // Initial node U826 - G831 from junction 
BasepairNode | Deletion Probability [0.0000000006195971] | Pair Probability [[0.010547588,0.013956235,0.013207310,0.061771316,0.000000000],[0.245853224,0.023971034,0.076912099,0.015069266,0.000000000],[0.013477701,0.062338547,0.002986305,0.015528739,0.000000000],[0.101411502,0.013901952,0.316578930,0.012488251,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.062500000,0.312500000,0.062500000,0.562500000,0.000000000] | Right Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.312500000,0.062500000,0.562500000,0.062500000,0.000000000] | Left Index [1] | Right Index [4] // Basepair U826 - G831 cWW 
HairpinNode  | Num Bases [2] | Left Index [2] | Right Index [3] | Norm Constant [1.000000000000000] // Hairpin node U828:A829
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.062500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.312500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U828
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.187500000,0.000000000,0.000000000,0.000000000],[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_15942.4:
> HL_15942.4 HL_5J7L_157 U  826 G  831
UUUAGG
> HL_15942.4 HL_4WF9_025 U  871 G  876
UUUAGG
> HL_15942.4 HL_4Y4O_127 U  826 G  831
UUUAGG
> HL_15942.4 HL_5TBW_022 C  958 G  963
CCUCAG
> HL_15942.4 HL_4V9F_026 U  919 G  924
UCGAAG
> HL_15942.4 HL_7A0S_024 U  839 G  844
UUGAGG