Alignment of HL_78457.3 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
6

3
7
6
I

8
7

4
9
6
I

10
6

5
11
5
I

12
4

6
13
3
I

14
3

7
15
2
I

16
2

8
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_78457.3_Instance_1 HL_78457.3_HL_4V9F_037_G1498_C1507GUUAAUAUUC
HL_78457.3_Sequence_1 HL_78457.3_HL_4V9F_037_G_1498_C_1507GUUAAUAUUCtrue100000.00
HL_78457.3_Instance_2 HL_78457.3_HL_5J7L_168_G1389_C1398GUUAAUAUUC
HL_78457.3_Sequence_2 HL_78457.3_HL_5J7L_168_G_1389_C_1398GUUAAUAUUCtrue100000.00
HL_78457.3_Instance_3 HL_78457.3_HL_4Y4O_137_G1389_C1398GUUAAUAUUC
HL_78457.3_Sequence_3 HL_78457.3_HL_4Y4O_137_G_1389_C_1398GUUAAUAUUCtrue100000.00
HL_78457.3_Instance_4 HL_78457.3_HL_4WF9_035_G1426_C1435GUUGAUAUUC
HL_78457.3_Sequence_4 HL_78457.3_HL_4WF9_035_G_1426_C_1435GUUGAUAUUCtrue92001.30
HL_78457.3_Instance_5 HL_78457.3_HL_5TBW_035_G1599_C1608GUUAAGAUUC
HL_78457.3_Sequence_5 HL_78457.3_HL_5TBW_035_G_1599_C_1608GUUAAGAUUCtrue93001.10
HL_78457.3_Instance_6 HL_78457.3_HL_5X2G_003_G73_C81GUUACAAUC
HL_78457.3_Sequence_6 HL_78457.3_HL_5X2G_003_G73_C81GUUACAAUCtrue84002.67

Conserved interactions between motif group positions in HL_78457.3:
1 2 s35 
1 8 cWW 
2 7 tWH 
3 5 tSH 
3 6 s55 
4 5 s35 
6 7 s35 
7 8 s35 
3 6 6BPh
JAR3D SCFG/MRF model for HL_78457.3:
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 [8] // Initial node G1498 - C1507 from junction 
BasepairNode | Deletion Probability [0.0000000014888525] | Pair Probability [[0.009366383,0.019506822,0.010665810,0.193723744,0.000000000],[0.016452306,0.009184679,0.195365254,0.012782718,0.000000000],[0.010547361,0.257647718,0.002010439,0.025755166,0.000000000],[0.191244451,0.013267227,0.022575563,0.009904357,0.000000000],[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 [0.001365561,0.170695070,0.820701898,0.006896081,0.000341390] | Right Letter Distribution [0.038461538,0.038461538,0.038461538,0.884615385,0.000000000] | Left Index [1] | Right Index [8] // Basepair G1498 - C1507 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.018067094,0.003998277,0.018765634,0.003998277,0.000000000],[0.040207941,0.322184696,0.003998277,0.003998277,0.000000000],[0.003998277,0.009584133,0.030406557,0.017782958,0.000000000],[0.456431444,0.003998277,0.023197522,0.039382361,0.000000000],[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 [2] | Right Index [7] // Basepair U1499 - A1504 tWH 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.187500000,0.062500000,0.187500000,0.562500000,0.000000000] | Position [2] | Left Index [3] | Right Index [6] // 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 [3] | Right Index [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.043836710,0.040040618,0.000486824,0.002394787,0.000000000],[0.044006054,0.041405452,0.000486824,0.000486824,0.000000000],[0.045269111,0.000486824,0.003008812,0.040415433,0.000000000],[0.387946550,0.342913643,0.003407767,0.003407767,0.000000000],[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 [3] | Right Index [5] // Basepair U1500 - A1502 tSH 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | Norm Constant [1.000000000000000] // Hairpin node A1501:A1501
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.687500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.187500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.062500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin conserved non-basepairing position A1501
Sequences of instances from HL_78457.3:
> HL_78457.3 HL_4V9F_037 G 1498 C 1507
GUUAAUAUUC
> HL_78457.3 HL_5J7L_168 G 1389 C 1398
GUUAAUAUUC
> HL_78457.3 HL_4Y4O_137 G 1389 C 1398
GUUAAUAUUC
> HL_78457.3 HL_4WF9_035 G 1426 C 1435
GUUGAUAUUC
> HL_78457.3 HL_5TBW_035 G 1599 C 1608
GUUAAGAUUC
> HL_78457.3 HL_5X2G_003 G   73 C   81
GUUACAAUC