Alignment of IL_06180.1 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
5

2
5
5
I

6
6

3
7
6
I

8
7

4
9
7
I

10
8


11
7
I

12
7

5
13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_06180.1_Instance_1 IL_06180.1_IL_4BPP_007_U63_A82UUCAGCGAAA
IL_06180.1_Sequence_1 IL_06180.1_IL_4BPP_007_U63_A82UUCAG*CGAAAtrue98000.26
IL_06180.1_Instance_2 IL_06180.1_IL_3U5F_007_U64_A86UAUAAGUGAAA
IL_06180.1_Sequence_2 IL_06180.1_IL_3U5F_007_U64_A86UAUAAG*UGAAAtrue100000.00
IL_06180.1_Instance_3 IL_06180.1_IL_4A1B_075_C1726_G1768CUAUGUGUAUG
IL_06180.1_Sequence_3 IL_06180.1_IL_4A1B_075_C_1726_G_1768CUAUG*UGUAUGtrue82001.94

Conserved interactions between motif group positions in IL_06180.1:
1 9 cWW 
2 3 s35 
2 6 s33 
2 7 tWH 
2 8 s55 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
8 9 s35 
3 6 6BR
JAR3D SCFG/MRF model for IL_06180.1:
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 [9] // Initial node U63 - A82 from junction 
BasepairNode | Deletion Probability [0.0000038011627649] | Pair Probability [[0.009329508,0.018973088,0.010330785,0.200366695,0.000000000],[0.023032249,0.009121783,0.208662517,0.011447685,0.000000000],[0.010390909,0.196046055,0.002131601,0.023465306,0.000000000],[0.225487075,0.011181893,0.027495044,0.012537807,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.993970181,0.005999820,0.000029999] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.657073038,0.336682053,0.005973391,0.000271518] | Right Letter Distribution [0.166666667,0.166666667,0.166666667,0.500000000,0.000000000] | Left Index [1] | Right Index [9] // Basepair U63 - A82 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Position [2] | Left Index [2] | Right Index [8] // 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 [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.209893082,0.004447947,0.173758185,0.004447947,0.000000000],[0.040350955,0.028229441,0.027807720,0.004447947,0.000000000],[0.004447947,0.004447947,0.053340127,0.028750700,0.000000000],[0.275527703,0.004447947,0.042813341,0.092841066,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair U64 - A80 tWH 
BasepairNode | Deletion Probability [0.0000006691671388] | Pair Probability [[0.105537798,0.106476768,0.202517886,0.114715851,0.000000000],[0.123017814,0.111603181,0.001271596,0.110514090,0.000000000],[0.001271596,0.001271596,0.006160615,0.001271596,0.000000000],[0.006055177,0.001271596,0.105771244,0.001271596,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.334863624,0.653524170,0.011072104,0.000540103] | Left Letter Distribution [0.375000000,0.125000000,0.125000000,0.375000000,0.000000000] | Right Length Distribution [0.993970181,0.005999820,0.000029999] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [6] // Basepair A66 - G79 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.014258858,0.211706755,0.014176550,0.093357766,0.000000000],[0.015234759,0.010399964,0.094014042,0.014566320,0.000000000],[0.013899989,0.109909176,0.002989625,0.256526531,0.000000000],[0.088532666,0.015883070,0.017860543,0.026683387,0.000000000],[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 G67 - C78 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_06180.1:
> IL_06180.1 IL_4BPP_007 U   63 A   82
UUCAG*CGAAA
> IL_06180.1 IL_3U5F_007 U   64 A   86
UAUAAG*UGAAA
> IL_06180.1 IL_4A1B_075 C 1726 G 1768
CUAUG*UGUAUG