Alignment of HL_56677.4 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
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
7

6
13
7
I

14
7

7
15
6
I

16
6

8
17
5
I

18
5

9
19
4
I

20
3

10
21
3
I

22
3

11
23
3
I

24
3

12
25
2
I

26
2

13
27
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_56677.4_Instance_1 HL_56677.4_HL_4V9F_068_C2780_G2794CUGAACGCAUCUAAG
HL_56677.4_Sequence_1 HL_56677.4_HL_4V9F_068_C_2780_G_2794CUGAACGCAUCUAAGtrue99000.30
HL_56677.4_Instance_2 HL_56677.4_HL_5J7L_199_C2745_G2759CUGAAAGCAUCUAAG
HL_56677.4_Sequence_2 HL_56677.4_HL_5J7L_199_C_2745_G_2759CUGAAAGCAUCUAAGtrue100000.00
HL_56677.4_Instance_3 HL_56677.4_HL_4WF9_062_C2772_G2786CUGAAAGCAUCUAAG
HL_56677.4_Sequence_3 HL_56677.4_HL_4WF9_062_C_2772_G_2786CUGAAAGCAUCUAAGtrue100000.00
HL_56677.4_Instance_4 HL_56677.4_HL_5TBW_067_C3110_G3124CUGAACGCCUCUAAG
HL_56677.4_Sequence_4 HL_56677.4_HL_5TBW_067_C_3110_G_3124CUGAACGCCUCUAAGtrue93001.61
HL_56677.4_Instance_5 HL_56677.4_HL_4Y4O_169_C2745_G2759CUGAAAGCAUCUAAG
HL_56677.4_Sequence_5 HL_56677.4_HL_4Y4O_169_C_2745_G_2759CUGAAAGCAUCUAAGtrue100000.00
HL_56677.4_Instance_6 HL_56677.4_HL_7A0S_065_C2725_G2739CUGAAAGCAUCUAAG
HL_56677.4_Sequence_6 HL_56677.4_HL_7A0S_065_C_2725_G_2739CUGAAAGCAUCUAAGtrue100000.00

Conserved interactions between motif group positions in HL_56677.4:
1 2 s35 
1 13 cWW 
2 3 s35 
2 10 tWH 
2 12 tSH 
2 13 s55 
3 4 s35 
3 9 s33 
3 10 s55 
3 11 tSH 
4 5 s35 
4 9 tHW 
4 11 s55 
5 6 s33 
5 8 tHW 
6 7 tSW 
7 8 s35 
8 9 s35 
10 11 s53 
10 12 cWH 
10 13 s35 
11 12 s35 
12 13 s35 
3 10 6BPh
11 3 6BR
7 6 7BR
JAR3D SCFG/MRF model for HL_56677.4:
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 [13] // Initial node C2780 - G2794 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009176708,0.016456041,0.010549755,0.191287868,0.000000000],[0.019511251,0.009346211,0.257693361,0.013270239,0.000000000],[0.010668232,0.195409608,0.002010896,0.022580688,0.000000000],[0.193767724,0.012785620,0.025761014,0.009724784,0.000000000],[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 [13] // Basepair C2780 - G2794 cWW 
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [2] | Num Right Bases [3] | Left Index [2] | Right Index [12] | Norm Constant [0.031373098575383] // Cluster node U2781:G2782 and U2791:A2793
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.018340435,0.003764121,0.032657415,0.003764121,0.000000000],[0.325525626,0.043924416,0.003764121,0.003764121,0.000000000],[0.003764121,0.011778114,0.024206194,0.035508032,0.000000000],[0.037075964,0.003764121,0.015383236,0.433015844,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2781 - U2791 tWH 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.042049014,0.044514549,0.000504770,0.002378984,0.000000000],[0.042361408,0.044411471,0.000504770,0.000504770,0.000000000],[0.409943044,0.003533393,0.017273635,0.299901013,0.000000000],[0.046937930,0.044171708,0.000504770,0.000504770,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2782 - A2792 tSH 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.115848656,0.105816603,0.001286545,0.006328779,0.000000000],[0.116296186,0.109423494,0.001286545,0.001286545,0.000000000],[0.119634107,0.001286545,0.007951482,0.106807141,0.000000000],[0.185258265,0.118916017,0.001286545,0.001286545,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2781 - A2793 tSH 
Interaction  | Interacting Bases [3,5] | Pair Probability [[0.002952495,0.002952495,0.012723357,0.012783050,0.000000000],[0.002952495,0.014198277,0.002952495,0.279650968,0.000000000],[0.010877559,0.002952495,0.010204484,0.002952495,0.000000000],[0.351853281,0.002952495,0.273191467,0.013850093,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U2791 - A2793 cWH 
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 [0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.062500000,0.812500000,0.062500000,0.062500000,0.000000000] | Left Index [4] | Right Index [9] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.018067094,0.040207941,0.003998277,0.456431444,0.000000000],[0.003998277,0.322184696,0.009584133,0.003998277,0.000000000],[0.018765634,0.003998277,0.030406557,0.023197522,0.000000000],[0.003998277,0.003998277,0.017782958,0.039382361,0.000000000],[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 [4] | Right Index [9] // Basepair A2783 - U2789 tHW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.342039969,0.091806375,0.003474987,0.018889658,0.000000000],[0.003474987,0.016497440,0.009191710,0.003474987,0.000000000],[0.272247212,0.003474987,0.111751524,0.016484687,0.000000000],[0.003474987,0.003474987,0.036339973,0.063901528,0.000000000],[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 [5] | Right Index [8] // Basepair A2784 - A2788 tHW 
HairpinNode  | Num Bases [2] | Left Index [6] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node C2785:C2787
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.024910016,0.240216583,0.003306393,0.016354853,0.000000000],[0.149732358,0.178534718,0.003306393,0.017293195,0.000000000],[0.149236317,0.003306393,0.003306393,0.011795353,0.000000000],[0.024035321,0.138536536,0.018365350,0.017763828,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction C2785 - C2787 tSW 
Insertion    | Location [1] | Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000]// Insertion in Hairpin after nucleotide 6, position 1
Sequences of instances from HL_56677.4:
> HL_56677.4 HL_4V9F_068 C 2780 G 2794
CUGAACGCAUCUAAG
> HL_56677.4 HL_5J7L_199 C 2745 G 2759
CUGAAAGCAUCUAAG
> HL_56677.4 HL_4WF9_062 C 2772 G 2786
CUGAAAGCAUCUAAG
> HL_56677.4 HL_5TBW_067 C 3110 G 3124
CUGAACGCCUCUAAG
> HL_56677.4 HL_4Y4O_169 C 2745 G 2759
CUGAAAGCAUCUAAG
> HL_56677.4 HL_7A0S_065 C 2725 G 2739
CUGAAAGCAUCUAAG