Alignment of IL_05684.1 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
7

3
7
7
I

8
8

4
9
8
I

10
9


11
8
I

12
8

5
13
7
I

14
7

6
15
6
I

16
5

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_05684.1_Instance_1 IL_05684.1_IL_3BNP_003_C5_G18CACCGCAAG
IL_05684.1_Sequence_1 IL_05684.1_IL_3BNP_003_C5_G18CACC*GCAAGtrue100000.00
IL_05684.1_Instance_2 IL_05684.1_IL_3BNP_002_C6_G17CACCGCAAG
IL_05684.1_Sequence_2 IL_05684.1_IL_3BNP_002_C6_G17CACC*GCAAGtrue100000.00
IL_05684.1_Instance_3 IL_05684.1_IL_3BNQ_005_C7_G19CACCGCAAG
IL_05684.1_Sequence_3 IL_05684.1_IL_3BNQ_005_C7_G19CACC*GCAAGtrue100000.00
IL_05684.1_Instance_4 IL_05684.1_IL_2QBG_057_U1468_G1524UAAGUGAUG
IL_05684.1_Sequence_4 IL_05684.1_IL_2QBG_057_U_1468_G_1524UAAG*UGAUGtrue88001.45
IL_05684.1_Instance_5 IL_05684.1_IL_3V2F_043_U1240_G1206UAAGCGAUG
IL_05684.1_Sequence_5 IL_05684.1_IL_3V2F_043_U_1240_G_1206UAAG*CGAUGtrue93000.81

Conserved interactions between motif group positions in IL_05684.1:
1 7 s35 
1 8 cWW 
2 3 s35 
2 6 s33 
3 4 s35 
3 6 tHS 
4 5 cWW 
5 6 s35 
6 7 s33 
7 8 s55 
JAR3D SCFG/MRF model for IL_05684.1:
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 [8] // Initial node C5 - G18 from junction 
BasepairNode | Deletion Probability [0.0000001230289089] | Pair Probability [[0.010904993,0.015774246,0.012839185,0.127192867,0.000000000],[0.135276838,0.011234809,0.171466677,0.014903175,0.000000000],[0.013062604,0.136650032,0.002624031,0.019883418,0.000000000],[0.130523585,0.013857958,0.172213082,0.011592499,0.000000000],[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 [0.009799118,0.979911808,0.009799118,0.000489956] | Right Letter Distribution [0.500000000,0.071428571,0.071428571,0.357142857,0.000000000] | Left Index [1] | Right Index [8] // Basepair C5 - G18 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [1] | Left Index [2] | Right Index [7] // 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 [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.785714286,0.071428571,0.071428571,0.071428571,0.000000000] | Position [2] | Left Index [3] | Right Index [7] // 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 [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.088238881,0.104302184,0.145760343,0.116988883,0.000000000],[0.124232993,0.211045704,0.001329649,0.115356801,0.000000000],[0.001329649,0.001329649,0.006210180,0.001329649,0.000000000],[0.006083401,0.001329649,0.073802737,0.001329649,0.000000000],[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 [6] // Basepair C7 - C15 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011033085,0.074348218,0.012113716,0.158408284,0.000000000],[0.018262496,0.008870795,0.201792114,0.013691727,0.000000000],[0.012104519,0.181373891,0.002341722,0.095844836,0.000000000],[0.157531112,0.013758912,0.023639681,0.014884893,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | 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 [4] | Right Index [5] // Basepair C8 - G14 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | Norm Constant [1.000000000000000] // Hairpin node type *
Interaction  | Interacting Bases [1,1] | Pair Probability [[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,1.000000000]] // Hairpin for truncation
Sequences of instances from IL_05684.1:
> IL_05684.1 IL_3BNP_003 C    5 G   18
CACC*GCAAG
> IL_05684.1 IL_3BNP_002 C    6 G   17
CACC*GCAAG
> IL_05684.1 IL_3BNQ_005 C    7 G   19
CACC*GCAAG
> IL_05684.1 IL_2QBG_057 U 1468 G 1524
UAAG*UGAUG
> IL_05684.1 IL_3V2F_043 U 1240 G 1206
UAAG*CGAUG