Alignment of IL_25380.1 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
5

3
7
5
I

8
6


9
5
I

10
5

4
11
4
I

12
3

5
13
3
I

14
3

6
15
3
I

16
3

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_25380.1_Instance_1 IL_25380.1_IL_4GXY_009_C105_G126CACGGAAG
IL_25380.1_Sequence_1 IL_25380.1_IL_4GXY_009_C105_G126CAC*GGAAGtrue75002.66
IL_25380.1_Instance_2 IL_25380.1_IL_4GMA_007_C113_G132CACGGAAG
IL_25380.1_Sequence_2 IL_25380.1_IL_4GMA_007_C113_G132CAC*GGAAGtrue75002.66
IL_25380.1_Instance_3 IL_25380.1_IL_4BPP_071_A1317_U1350ACUAGCUUCU
IL_25380.1_Sequence_3 IL_25380.1_IL_4BPP_071_A_1317_U_1350ACUAG*CUUCUtrue57004.64
IL_25380.1_Instance_4 IL_25380.1_IL_4IOA_088_A2438_U2472AUCGGUUU
IL_25380.1_Sequence_4 IL_25380.1_IL_4IOA_088_A_2438_U_2472AUC*GGUUUtrue100000.00
IL_25380.1_Instance_5 IL_25380.1_IL_2XXA_009_G10_C93GUGCCUUC
IL_25380.1_Sequence_5 IL_25380.1_IL_2XXA_009_G10_C93GUG*CCUUCtrue100000.02
IL_25380.1_Instance_6 IL_25380.1_IL_2QBG_093_A2459_U2493AUAUGUUU
IL_25380.1_Sequence_6 IL_25380.1_IL_2QBG_093_A_2459_U_2493AUA*UGUUUtrue99000.14

Conserved interactions between motif group positions in IL_25380.1:
1 2 s35 
1 8 cWW 
2 3 s35 
2 7 cWW 
3 4 cWW 
4 5 s35 
5 7 cSH 
6 7 s35 
7 8 s35 
JAR3D SCFG/MRF model for IL_25380.1:
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 C105 - G126 from junction 
BasepairNode | Deletion Probability [0.0000040113606825] | Pair Probability [[0.009303385,0.020606440,0.010352389,0.224394684,0.000000000],[0.019084521,0.008572365,0.213736718,0.011538453,0.000000000],[0.010368187,0.203786078,0.002067853,0.025420108,0.000000000],[0.192395003,0.011467640,0.024007914,0.012898260,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.824969064,0.008249691,0.165337550,0.001374948,0.000068747] | Left Letter Distribution [0.125000000,0.375000000,0.125000000,0.375000000,0.000000000] | 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 [8] // Basepair C105 - G126 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [7] | Norm Constant [0.325985083110521] // Cluster node A106:A106 and G123:A125
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.090273333,0.187976707,0.013697566,0.032978943,0.000000000],[0.017577621,0.017891685,0.020685705,0.015101851,0.000000000],[0.013432372,0.021069153,0.004311624,0.043901633,0.000000000],[0.027693624,0.016392876,0.017551006,0.459464302,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A106 - A125 cWW 
Interaction  | Interacting Bases [2,4] | Pair Probability [[0.094625064,0.099445771,0.005326262,0.004472504,0.000000000],[0.092560928,0.100307341,0.001118543,0.140439759,0.000000000],[0.083930061,0.005637867,0.010582824,0.124852072,0.000000000],[0.025988045,0.109101383,0.001118543,0.100493033,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G123 - A125 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.312500000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.062500000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.062500000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.562500000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A124
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009579898,0.018858927,0.010968709,0.198510678,0.000000000],[0.018733316,0.008310552,0.229411558,0.012602551,0.000000000],[0.010989873,0.219102584,0.002068376,0.024744711,0.000000000],[0.187963655,0.012508405,0.024679279,0.010966928,0.000000000],[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 [3] | Right Index [4] // Basepair C107 - G122 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_25380.1:
> IL_25380.1 IL_4GXY_009 C  105 G  126
CAC*GGAAG
> IL_25380.1 IL_4GMA_007 C  113 G  132
CAC*GGAAG
> IL_25380.1 IL_4BPP_071 A 1317 U 1350
ACUAG*CUUCU
> IL_25380.1 IL_4IOA_088 A 2438 U 2472
AUC*GGUUU
> IL_25380.1 IL_2XXA_009 G   10 C   93
GUG*CCUUC
> IL_25380.1 IL_2QBG_093 A 2459 U 2493
AUA*UGUUU