Alignment of HL_67265.4 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
5

2
5
5
I

6
6

3
7
6
I

8
6

4
9
6
I

10
6

5
11
6
I

12
6

6
13
6
I

14
6

7
15
5
I

16
5

8
17
4
I

18
3

9
19
2
I

20
2

10
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_67265.4_Instance_1 HL_67265.4_HL_4LFB_001_U12_G22UUUGAUCCUGG
HL_67265.4_Sequence_1 HL_67265.4_HL_4LFB_001_U12_G22UUUGAUCCUGGtrue100000.00
HL_67265.4_Instance_2 HL_67265.4_HL_5J7L_001_U12_G22UUUGAUCAUGG
HL_67265.4_Sequence_2 HL_67265.4_HL_5J7L_001_U12_G22UUUGAUCAUGGtrue93001.47
HL_67265.4_Instance_3 HL_67265.4_HL_6CZR_072_U13_G23UUUGAUCCUGG
HL_67265.4_Sequence_3 HL_67265.4_HL_6CZR_072_U13_G23UUUGAUCCUGGtrue100000.00
HL_67265.4_Instance_4 HL_67265.4_HL_4V88_186_G7_C17GUUGAUCCUGC
HL_67265.4_Sequence_4 HL_67265.4_HL_4V88_186_G7_C17GUUGAUCCUGCtrue100000.04
HL_67265.4_Instance_5 HL_67265.4_HL_4XWF_002_C50_G60CGCCCGCCUGG
HL_67265.4_Sequence_5 HL_67265.4_HL_4XWF_002_C50_G60CGCCCGCCUGGtrue87002.58
HL_67265.4_Instance_6 HL_67265.4_HL_5X6B_002_G29_C39GACUGCAGAUC
HL_67265.4_Sequence_6 HL_67265.4_HL_5X6B_002_G29_C39GACUGCAGAUCtrue470010.55
HL_67265.4_Instance_7 HL_67265.4_HL_4ZNP_002_C58_G68CGACCGCCUGG
HL_67265.4_Sequence_7 HL_67265.4_HL_4ZNP_002_C58_G68CGACCGCCUGGtrue87002.58
HL_67265.4_Instance_8 HL_67265.4_HL_5BTP_004_C62_G72CGACCGUCUGG
HL_67265.4_Sequence_8 HL_67265.4_HL_5BTP_004_C62_G72CGACCGUCUGGtrue80004.05

Conserved interactions between motif group positions in HL_67265.4:
1 2 s33 
1 10 cWW 
2 8 tHW 
2 9 s55 
2 10 s35 
3 4 s35 
4 5 s35 
5 6 s35 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
JAR3D SCFG/MRF model for HL_67265.4:
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 [10] // Initial node U12 - G22 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009658782,0.015795790,0.011556619,0.131140048,0.000000000],[0.118367062,0.015592795,0.164727178,0.013699441,0.000000000],[0.011681863,0.152918877,0.002404351,0.019826839,0.000000000],[0.148769631,0.013160068,0.159891367,0.010809289,0.000000000],[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 U12 - G22 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.050000000,0.050000000,0.750000000,0.150000000,0.000000000] | Position [2] | Left Index [2] | Right Index [9] // Fixed node on right
InitialNode  | Left Length Distribution [1.000000000] | 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 [8] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000001232656381] | Pair Probability [[0.046667391,0.290452158,0.003358559,0.033081247,0.000000000],[0.003358559,0.039191819,0.010509091,0.003358559,0.000000000],[0.029138771,0.003358559,0.021598119,0.104634874,0.000000000],[0.003358559,0.003358559,0.031682250,0.372892925,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.006170935,0.987349583,0.006170935,0.000308547] | Left Letter Distribution [0.250000000,0.250000000,0.050000000,0.450000000,0.000000000] | 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 [8] // Basepair U13 - U20 tHW 
HairpinNode  | Num Bases [5] | Left Index [3] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G15:C19
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.350000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.450000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.450000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.350000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A16
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.050000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.150000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.350000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.450000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U17
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.650000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.050000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.150000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C18
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.150000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.650000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.150000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.050000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C19
Sequences of instances from HL_67265.4:
> HL_67265.4 HL_4LFB_001 U   12 G   22
UUUGAUCCUGG
> HL_67265.4 HL_5J7L_001 U   12 G   22
UUUGAUCAUGG
> HL_67265.4 HL_6CZR_072 U   13 G   23
UUUGAUCCUGG
> HL_67265.4 HL_4V88_186 G    7 C   17
GUUGAUCCUGC
> HL_67265.4 HL_4XWF_002 C   50 G   60
CGCCCGCCUGG
> HL_67265.4 HL_5X6B_002 G   29 C   39
GACUGCAGAUC
> HL_67265.4 HL_4ZNP_002 C   58 G   68
CGACCGCCUGG
> HL_67265.4 HL_5BTP_004 C   62 G   72
CGACCGUCUGG