Alignment of HL_90620.1 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
3
I

6
4

3
7
5
I

8
8

4
9
8
I

10
9

5
11
9
I

12
9

6
13
9
I

14
9

7
15
8
I

16
8

8
17
7
I

18
6

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_90620.1_Instance_1 HL_90620.1_HL_3IVN_003_A49_U59AACCGUAAAAU
HL_90620.1_Sequence_1 HL_90620.1_HL_3IVN_003_A49_U59AACCGUAAAAUtrue100000.00
HL_90620.1_Instance_2 HL_90620.1_HL_6P2H_002_A59_U69AACCGUAAAAU
HL_90620.1_Sequence_2 HL_90620.1_HL_6P2H_002_A59_U69AACCGUAAAAUtrue100000.00

Conserved interactions between motif group positions in HL_90620.1:
1 2 s35 
1 11 cWW 
2 3 s35 
2 10 cWW 
2 11 s55 
3 4 s35 
4 8 cSW 
5 6 cSH 
6 7 s53 
7 8 s35 
8 9 s35 
9 10 s35 
10 11 s35 
JAR3D SCFG/MRF model for HL_90620.1:
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 A49 - U59 from junction 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.009282926,0.022010543,0.009914366,0.223723012,0.000000000],[0.017518170,0.009580259,0.194165974,0.010358839,0.000000000],[0.009895067,0.196683142,0.002041152,0.053213779,0.000000000],[0.196023621,0.011028161,0.023012614,0.011548375,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [11] // Basepair A49 - U59 cWW 
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.615264647,0.027680686,0.049320315,0.027089794,0.000000000],[0.018530781,0.010338068,0.027182752,0.026285801,0.000000000],[0.037714972,0.027750896,0.005956568,0.029081265,0.000000000],[0.026324389,0.029605623,0.020261781,0.021611660,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [10] // Basepair A50 - A58 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.125000000,0.625000000,0.125000000,0.125000000,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left
InitialNode  | Left Length Distribution [0.991950402,0.007999600,0.000049998] | 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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.625000000,0.125000000,0.125000000,0.125000000,0.000000000] | Position [2] | Left Index [4] | 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 [0.991950402,0.007999600,0.000049998] | 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
BasepairNode | Deletion Probability [0.0000229437914523] | Pair Probability [[0.199412271,0.019366427,0.018103352,0.007852611,0.000000000],[0.236401213,0.017190312,0.002167934,0.008384066,0.000000000],[0.199173117,0.002167934,0.053682368,0.006678898,0.000000000],[0.195352999,0.016756688,0.009592831,0.007716981,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.991950402,0.007999600,0.000049998] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.991950402,0.007999600,0.000049998] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [8] // Basepair C52 - A56 cSW 
HairpinNode  | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [1.000000000000000] // Hairpin node G53:A55
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.079296878,0.080799881,0.004442628,0.078964610,0.000000000],[0.059200300,0.089215891,0.000983673,0.079130149,0.000000000],[0.069281848,0.000983673,0.084512044,0.117975163,0.000000000],[0.080527243,0.080043827,0.000983673,0.093658519,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction G53 - U54 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.625000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.125000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.125000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.125000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A55
Sequences of instances from HL_90620.1:
> HL_90620.1 HL_3IVN_003 A   49 U   59
AACCGUAAAAU
> HL_90620.1 HL_6P2H_002 A   59 U   69
AACCGUAAAAU