Alignment of HL_14757.1 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
4
I

6
5

3
7
6
I

8
11

4
9
11
I

10
11

5
11
11
I

12
11

6
13
11
I

14
11

7
15
11
I

16
11

8
17
11
I

18
11

9
19
12
I

20
13

10
21
12
I

22
11

11
23
11
I

24
11

12
25
11
I

26
11

13
27
11
I

28
11

14
29
10
I

30
9

15
31
8
I

32
7

16
33
2
I

34
2

17
35
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
HL_14757.1_Instance_1 HL_14757.1,HL_6RTI_001,C15_G32CCUGACUUCUAUACUAAG
HL_14757.1_Sequence_1 HL_14757.16RTI_C15_G32CCUGACUUCUAUACUAAGtrue100000.00

Conserved interactions between motif group positions in HL_14757.1:
1 2 s35 
1 17 cWW 
2 3 s35 
2 17 s55 
3 14 s33 
4 8 tSW 
4 12 s35 
4 13 tWW 
4 14 s55 
5 6 s55 
5 9 s53 
5 10 s35 
5 11 tHW 
7 8 s35 
7 14 cWW 
7 15 s55 
8 9 s35 
9 11 s33 
9 13 tSW 
11 12 s33 
15 16 s35 
16 17 s35 
12 5 6BPh
6 9 6BPh
8 4 7BR
JAR3D SCFG/MRF model for HL_14757.1:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [17] // Initial node
BasepairNode | Deletion Probability [0.0000224390099112] | Pair Probability [[0.009631000,0.017270697,0.011072020,0.200757565,0.000000000],[0.020477154,0.009808895,0.220945507,0.013927182,0.000000000],[0.011196362,0.205083350,0.002110445,0.023698544,0.000000000],[0.203360186,0.013418572,0.027036311,0.010206209,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [17] // Basepair C15 - G32 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | Position [1] | Left Index [2] | Right Index [16] // Fixed node on left for 6RTI|1|X|CFZ|16
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [3] | Right Index [16] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Position [1] | Left Index [3] | Right Index [16] // Fixed node on left for 6RTI|1|X|UFT|17
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | 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 [16] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [16] // Fixed node on right for 6RTI|1|X|A|30
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [15] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Position [2] | Left Index [4] | Right Index [15] // Fixed node on right for 6RTI|1|X|UFT|29
InitialNode  | Left Length Distribution [1.000000000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [14] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.000000000000000000000000047668834931106073124306225301151164] | Num Left Bases [6] | Num Right Bases [4] | Left Index [4] | Right Index [14] | Norm Constant [0.391790947925516] // Cluster node 6RTI|1|X|G|18:6RTI|1|X|UFT|24 and 6RTI|1|X|UFT|26:6RTI|1|X|UFT|29
Interaction  | Interacting Bases [2,7] | Pair Probability [[0.018961504,0.042198433,0.004196211,0.429522110,0.000000000],[0.004196211,0.338134433,0.010058595,0.004196211,0.000000000],[0.019694625,0.004196211,0.031911832,0.024345914,0.000000000],[0.004196211,0.004196211,0.018663303,0.041331983,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6RTI|1|X|A|19 - 6RTI|1|X|UFT|26 tHW 
Interaction  | Interacting Bases [1,9] | Pair Probability [[0.019248776,0.025161547,0.006453964,0.031991442,0.000000000],[0.018937138,0.031225092,0.026419516,0.032085020,0.000000000],[0.006453964,0.655297410,0.019283858,0.027194782,0.000000000],[0.026877625,0.030580008,0.020964892,0.021824965,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6RTI|1|X|G|18 - 6RTI|1|X|CFZ|28 tWW 
Interaction  | Interacting Bases [6,9] | Pair Probability [[0.023045587,0.015735122,0.003850137,0.038297823,0.000000000],[0.017385760,0.331041442,0.003850137,0.049396378,0.000000000],[0.016732538,0.003850137,0.003850137,0.016931924,0.000000000],[0.017611485,0.394914698,0.018526368,0.044980327,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6RTI|1|X|UFT|24 - 6RTI|1|X|CFZ|28 tSW 
Interaction  | Interacting Bases [4,10] | Pair Probability [[0.015580470,0.285764820,0.013910732,0.024295965,0.000000000],[0.017220118,0.018567546,0.020767248,0.015270770,0.000000000],[0.013620185,0.021155527,0.004294262,0.054860011,0.000000000],[0.021224145,0.016538232,0.017602771,0.439327198,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6RTI|1|X|UFT|22 - 6RTI|1|X|UFT|29 cWW 
Interaction  | Interacting Bases [1,5] | Pair Probability [[0.007482036,0.007482036,0.007482036,0.007482036,0.000000000],[0.007482036,0.007482036,0.137146856,0.007482036,0.000000000],[0.007482036,0.758104634,0.007482036,0.007482036,0.000000000],[0.007482036,0.007482036,0.007482036,0.007482036,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction 6RTI|1|X|G|18 - 6RTI|1|X|CFZ|23 tSW 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.055555556,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.833333333,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion 6RTI|1|X|UFT|21
Interaction  | Interacting Bases [8,8] | Pair Probability [[0.833333333,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.055555556,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.055555556,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.055555556,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion 6RTI|1|X|A|27
Insertion    | Location [2] | Length Distribution [0.045351474,0.907029478,0.045351474,0.002267574] | Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000]// Insertion after nucleotide 5, position 2 in cluster node
InitialNode  | Left Length Distribution [0.989901010,0.009999000,0.000099990] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.989901010,0.009999000,0.000099990] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [10] | Right Index [10] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [10] | Right Index [10] | Norm Constant [1.000000000000000] // Hairpin node A25:A25
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.166666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.166666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.166666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A25
Sequences of instances from HL_14757.1:
> HL_14757.1  6RTI C   15 G   32
CCUGACUUCUAUACUAAG