Alignment of HL_04171.2 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
4

3
7
5
I

8
7
I

9
8

4
10
8
I

11
8

5
12
8
I

13
8

6
14
8
I

15
8

7
16
7
I

17
6

8
18
3
I

19
3

9
20
2
I

21
2

10
22
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
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distance

Alignment
score
deficit
HL_04171.2_Instance_1 HL_04171.2_HL_5SWD_004_A30_U40AUGAUAUGGUU
HL_04171.2_Sequence_1 HL_04171.2_HL_5SWD_004_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.2_Instance_2 HL_04171.2_HL_3LA5_001_A30_U40AUGAUAUGGUU
HL_04171.2_Sequence_2 HL_04171.2_HL_3LA5_001_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.2_Instance_3 HL_04171.2_HL_4LX6_001_A30_U40AUGAUAUGGUU
HL_04171.2_Sequence_3 HL_04171.2_HL_4LX6_001_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.2_Instance_4 HL_04171.2_HL_1Y26_001_A30_U40AUGAUAUGGUU
HL_04171.2_Sequence_4 HL_04171.2_HL_1Y26_001_A30_U40AUGAUAUGGUUtrue100000.00
HL_04171.2_Instance_5 HL_04171.2_HL_3IVN_001_A21_U31AUGAUAUGGUU
HL_04171.2_Sequence_5 HL_04171.2_HL_3IVN_001_A21_U31AUGAUAUGGUUtrue100000.00
HL_04171.2_Instance_6 HL_04171.2_HL_4ATO_003_U15_A25UUACCGUAGUA
HL_04171.2_Sequence_6 HL_04171.2_HL_4ATO_003_U15_A25UUACCGUAGUAtrue95000.96
HL_04171.2_Instance_7 HL_04171.2_HL_4ATO_001_U15_A25UUACCGUAGUA
HL_04171.2_Sequence_7 HL_04171.2_HL_4ATO_001_U15_A25UUACCGUAGUAtrue95000.96
HL_04171.2_Instance_8 HL_04171.2_HL_4ATO_002_U15_A25UUACCGUAGUA
HL_04171.2_Sequence_8 HL_04171.2_HL_4ATO_002_U15_A25UUACCGUAGUAtrue95000.96
HL_04171.2_Instance_9 HL_04171.2_HL_2D6F_004_G912_C923GUAGUGGUAAUC
HL_04171.2_Sequence_9 HL_04171.2_HL_2D6F_004_G912_C923GUAGUGGUAAUCtrue61007.06

Conserved interactions between motif group positions in HL_04171.2:
1 2 s35 
1 10 cWW 
2 3 s35 
2 9 cWW 
2 10 s55 
3 4 s35 
3 9 s55 
4 5 s35 
4 7 cSS 
5 7 cSS 
6 7 s55 
7 8 s35 
9 10 s35 
JAR3D SCFG/MRF model for HL_04171.2:
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 [10] // Initial node A30 - U40 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008656101,0.019023238,0.009397950,0.234156706,0.000000000],[0.017761122,0.009039756,0.183496187,0.010211739,0.000000000],[0.009381147,0.193806354,0.001916039,0.037636721,0.000000000],[0.213861372,0.010402960,0.031027090,0.010225516,0.000000000],[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 [10] // Basepair A30 - U40 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014436950,0.264791255,0.012889761,0.022512775,0.000000000],[0.015956256,0.017204790,0.019243046,0.014149980,0.000000000],[0.012620538,0.019602827,0.003979087,0.050833588,0.000000000],[0.019666410,0.015324417,0.016310825,0.480477495,0.000000000],[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 [2] | Right Index [9] // Basepair U31 - U39 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.409090909,0.045454545,0.500000000,0.045454545,0.000000000] | Position [1] | Left Index [3] | Right Index [8] // Fixed node on left
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.136363636,0.045454545,0.772727273,0.045454545,0.000000000] | Position [2] | Left Index [4] | Right Index [8] // Fixed node on right
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 [4] | Right Index [7] // New Initial node after Fixed node
HairpinNode  | Num Bases [4] | Left Index [4] | Right Index [7] | Norm Constant [0.261529643730035] // Hairpin node A33:G37
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.071703980,0.073208534,0.132869395,0.072674192,0.000000000],[0.099926616,0.073031471,0.003157041,0.066347042,0.000000000],[0.093619001,0.003097427,0.006610608,0.071752232,0.000000000],[0.067116411,0.034167437,0.059908779,0.070809834,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction A33 - G37 cSS 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.071212161,0.071893141,0.072699428,0.066762370,0.000000000],[0.099834189,0.072423742,0.003167868,0.055492012,0.000000000],[0.069797814,0.003219472,0.007219597,0.061775210,0.000000000],[0.091529489,0.065448457,0.119896235,0.067628816,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U34 - G37 cSS 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.045454545,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.409090909,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.045454545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A35
Insertion    | Location [3] | Length Distribution [0.004882663,0.879489762,0.114742592,0.000854466,0.000030517] | Letter Distribution [0.041666667,0.041666667,0.125000000,0.791666667,0.000000000]// Insertion in Hairpin after nucleotide 6, position 3
Sequences of instances from HL_04171.2:
> HL_04171.2 HL_5SWD_004 A   30 U   40
AUGAUAUGGUU
> HL_04171.2 HL_3LA5_001 A   30 U   40
AUGAUAUGGUU
> HL_04171.2 HL_4LX6_001 A   30 U   40
AUGAUAUGGUU
> HL_04171.2 HL_1Y26_001 A   30 U   40
AUGAUAUGGUU
> HL_04171.2 HL_3IVN_001 A   21 U   31
AUGAUAUGGUU
> HL_04171.2 HL_4ATO_003 U   15 A   25
UUACCGUAGUA
> HL_04171.2 HL_4ATO_001 U   15 A   25
UUACCGUAGUA
> HL_04171.2 HL_4ATO_002 U   15 A   25
UUACCGUAGUA
> HL_04171.2 HL_2D6F_004 G  912 C  923
GUAGUGGUAAUC