Alignment of HL_99402.3 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
4
I

6
5

3
7
6
I

8
7

4
9
8
I

10
12
I

11
13

5
12
13
I

13
13

6
14
13
I

15
13

7
16
12
I

17
11

8
18
10
I

19
9

9
20
2
I

21
2

10
22
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
HL_99402.3_Instance_1 HL_99402.3_HL_7A0S_001_C58_G67CGAUUACCUG
HL_99402.3_Sequence_1 HL_99402.3_HL_7A0S_001_C58_G67CGAUUACCUGtrue100000.00
HL_99402.3_Instance_2 HL_99402.3_HL_4V9F_001_U55_G64UGCCAAGCUG
HL_99402.3_Sequence_2 HL_99402.3_HL_4V9F_001_U55_G64UGCCAAGCUGtrue93001.29
HL_99402.3_Instance_3 HL_99402.3_HL_4Y4O_103_U59_G68UGGCUACCUG
HL_99402.3_Sequence_3 HL_99402.3_HL_4Y4O_103_U59_G68UGGCUACCUGtrue95000.99
HL_99402.3_Instance_4 HL_99402.3_HL_2XDB_001_U4_A13UGAUUUGCUA
HL_99402.3_Sequence_4 HL_99402.3_HL_2XDB_001_U4_A13UGAUUUGCUAtrue96000.67
HL_99402.3_Instance_5 HL_99402.3_HL_2XD0_006_U4_A13UGAUUUGCUA
HL_99402.3_Sequence_5 HL_99402.3_HL_2XD0_006_U4_A13UGAUUUGCUAtrue96000.67

Conserved interactions between motif group positions in HL_99402.3:
1 10 cWW 
2 5 s33 
3 4 s35 
5 6 cSH 
5 7 cSH 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35 
5 2 7BR
JAR3D SCFG/MRF model for HL_99402.3:
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 [10] // Initial node C58 - G67 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009733237,0.015573717,0.011528689,0.129390568,0.000000000],[0.130062747,0.016568213,0.143123808,0.013201463,0.000000000],[0.011681576,0.129441827,0.002485021,0.019215890,0.000000000],[0.171096022,0.012316634,0.173425084,0.011155504,0.000000000],[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 [10] // Basepair C58 - G67 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.785714286,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.214285714,0.214285714,0.071428571,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left
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 [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 [0.071428571,0.357142857,0.071428571,0.500000000,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left
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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.071428571,0.071428571,0.785714286,0.000000000] | Position [2] | Left Index [5] | 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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [5] | Right Index [8] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.071428571,0.785714286,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [5] | Right Index [8] // Fixed node on right
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 [5] | Right Index [7] // New Initial node after Fixed node
HairpinNode  | Num Bases [3] | Left Index [5] | Right Index [7] | Norm Constant [0.381499453226501] // Hairpin node U62:C64
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.109342186,0.092826534,0.004766805,0.027833881,0.000000000],[0.042129311,0.043253920,0.000483888,0.020439090,0.000000000],[0.020178040,0.000483888,0.040571218,0.042404139,0.000000000],[0.207785485,0.154312872,0.001857507,0.191331237,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U62 - A63 cSH 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.035831964,0.038458679,0.244702065,0.045671713,0.000000000],[0.028039444,0.028645287,0.000766058,0.005534633,0.000000000],[0.006054028,0.000766058,0.030015390,0.026547693,0.000000000],[0.131063903,0.172895117,0.080539105,0.124468863,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Hairpin Interaction U62 - C64 cSH 
Sequences of instances from HL_99402.3:
> HL_99402.3 HL_7A0S_001 C   58 G   67
CGAUUACCUG
> HL_99402.3 HL_4V9F_001 U   55 G   64
UGCCAAGCUG
> HL_99402.3 HL_4Y4O_103 U   59 G   68
UGGCUACCUG
> HL_99402.3 HL_2XDB_001 U    4 A   13
UGAUUUGCUA
> HL_99402.3 HL_2XD0_006 U    4 A   13
UGAUUUGCUA