Alignment of HL_35978.6 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
3
I

12
3

6
13
3
I

14
3

7
15
3
I

16
3

8
17
3
I

18
3

9
19
3
I

20
3

10
21
2
I

22
2

11
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_35978.6_Instance_1 HL_35978.6_HL_4C4W_002_C11_G22CAUUGCACUCCG
HL_35978.6_Sequence_1 HL_35978.6_HL_4C4W_002_C11_G22CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_2 HL_35978.6_HL_5FJ4_002_C11_G22CAUUGCACUCCG
HL_35978.6_Sequence_2 HL_35978.6_HL_5FJ4_002_C11_G22CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_3 HL_35978.6_HL_1U6B_003_C1002_G1013CAUUGCACUCCG
HL_35978.6_Sequence_3 HL_35978.6_HL_1U6B_003_C_1002_G_1013CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_4 HL_35978.6_HL_5DDP_002_C34_G45CAUUGCACUCCG
HL_35978.6_Sequence_4 HL_35978.6_HL_5DDP_002_C34_G45CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_5 HL_35978.6_HL_3HHN_008_C1004_G1015CAUUGCACUCCG
HL_35978.6_Sequence_5 HL_35978.6_HL_3HHN_008_C_1004_G_1015CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_6 HL_35978.6_HL_3CUL_002_C29_G40CAUUGCACUCCG
HL_35978.6_Sequence_6 HL_35978.6_HL_3CUL_002_C29_G40CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_7 HL_35978.6_HL_6F4H_001_C6_G17CAUUGCACCUCG
HL_35978.6_Sequence_7 HL_35978.6_HL_6F4H_001_C6_G17CAUUGCACCUCGtrue82003.98
HL_35978.6_Instance_8 HL_35978.6_HL_3G9C_005_C17A_G17LCAUUGCACUCCG
HL_35978.6_Sequence_8 HL_35978.6_HL_3G9C_005_C17A_G17LCAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_9 HL_35978.6_HL_4PKD_001_C64_G75CAUUGCACUCCG
HL_35978.6_Sequence_9 HL_35978.6_HL_4PKD_001_C64_G75CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_10 HL_35978.6_HL_5DDO_002_C34_G45CAUUGCACUCCG
HL_35978.6_Sequence_10 HL_35978.6_HL_5DDO_002_C34_G45CAUUGCACUCCGtrue100000.00
HL_35978.6_Instance_11 HL_35978.6_HL_6F4G_001_U8_G20UAUUGCAGUACCG
HL_35978.6_Sequence_11 HL_35978.6_HL_6F4G_001_U8_G20UAUUGCAGUACCGtrue64008.05
HL_35978.6_Instance_12 HL_35978.6_HL_3IWN_002_C57_G68CAUUGCACUCCG
HL_35978.6_Sequence_12 HL_35978.6_HL_3IWN_002_C57_G68CAUUGCACUCCGtrue100000.00

Conserved interactions between motif group positions in HL_35978.6:
1 2 s35 
1 11 cWW 
2 3 s35 
2 11 s55 
4 5 s55 
6 7 s35 
8 9 s35 
9 10 s35 
JAR3D SCFG/MRF model for HL_35978.6:
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 [11] // Initial node C11 - G22 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008814842,0.015337879,0.010236108,0.168782487,0.000000000],[0.039887656,0.010229656,0.275885847,0.012729598,0.000000000],[0.010362616,0.172347010,0.001995485,0.020703592,0.000000000],[0.174646453,0.012206329,0.056369083,0.009465356,0.000000000],[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 [11] // Basepair C11 - G22 cWW 
HairpinNode  | Num Bases [9] | Left Index [2] | Right Index [10] | Norm Constant [0.999999999999999] // Hairpin node A12:C21
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.892857143,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A12
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.892857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U13
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.892857143,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U14
Interaction  | Interacting Bases [4,4] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.035714286,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.892857143,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position G15
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.821428571,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.107142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A17
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.107142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.750000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.107142857,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C18
Interaction  | Interacting Bases [7,7] | Pair Probability [[0.107142857,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.107142857,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.750000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position U19
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.821428571,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.107142857,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C20
Interaction  | Interacting Bases [9,9] | Pair Probability [[0.035714286,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.892857143,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.035714286,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.035714286,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position C21
Insertion    | Location [4] | Length Distribution [0.086444414,0.909560546,0.003805621,0.000189420] | Letter Distribution [0.038461538,0.884615385,0.038461538,0.038461538,0.000000000]// Insertion in Hairpin after nucleotide 5, position 4
Insertion    | Location [6] | Length Distribution [0.829821046,0.169280730,0.000863677,0.000034547] | Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000]// Insertion in Hairpin after nucleotide 7, position 6
Sequences of instances from HL_35978.6:
> HL_35978.6 HL_4C4W_002 C   11 G   22
CAUUGCACUCCG
> HL_35978.6 HL_5FJ4_002 C   11 G   22
CAUUGCACUCCG
> HL_35978.6 HL_1U6B_003 C 1002 G 1013
CAUUGCACUCCG
> HL_35978.6 HL_5DDP_002 C   34 G   45
CAUUGCACUCCG
> HL_35978.6 HL_3HHN_008 C 1004 G 1015
CAUUGCACUCCG
> HL_35978.6 HL_3CUL_002 C   29 G   40
CAUUGCACUCCG
> HL_35978.6 HL_6F4H_001 C    6 G   17
CAUUGCACCUCG
> HL_35978.6 HL_3G9C_005 C  17A G  17L
CAUUGCACUCCG
> HL_35978.6 HL_4PKD_001 C   64 G   75
CAUUGCACUCCG
> HL_35978.6 HL_5DDO_002 C   34 G   45
CAUUGCACUCCG
> HL_35978.6 HL_6F4G_001 U    8 G   20
UAUUGCAGUACCG
> HL_35978.6 HL_3IWN_002 C   57 G   68
CAUUGCACUCCG