Alignment of IL_92114.3 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
7
I

10
8


11
7
I

12
7

5
13
4
I

14
3

6
15
3
I

16
3

7
17
3
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_92114.3_Instance_1 IL_92114.3_IL_1GID_007_U247_G227UAUGCUAAG
IL_92114.3_Sequence_1 IL_92114.3_IL_1GID_007_U247_G227UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_2 IL_92114.3_IL_1GID_014_U247_G227UAUGCUAAG
IL_92114.3_Sequence_2 IL_92114.3_IL_1GID_014_U247_G227UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_3 IL_92114.3_IL_3T4B_002_U17_G6UAUGCUAAG
IL_92114.3_Sequence_3 IL_92114.3_IL_3T4B_002_U17_G6UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_4 IL_92114.3_IL_1X8W_007_U247_G227UAUGCUAAG
IL_92114.3_Sequence_4 IL_92114.3_IL_1X8W_007_U247_G227UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_5 IL_92114.3_IL_1U6B_003_U80_G65UAUGCUAAG
IL_92114.3_Sequence_5 IL_92114.3_IL_1U6B_003_U80_G65UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_6 IL_92114.3_IL_2Y9B_003_U846_G860UAUGCUAAG
IL_92114.3_Sequence_6 IL_92114.3_IL_2Y9B_003_U846_G860UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_7 IL_92114.3_IL_4FAW_013_U332_G350UAUGCUAAG
IL_92114.3_Sequence_7 IL_92114.3_IL_4FAW_013_U332_G350UAUG*CUAAGtrue100000.00
IL_92114.3_Instance_8 IL_92114.3_IL_1NBS_008_U159_G150UAUGCUACG
IL_92114.3_Sequence_8 IL_92114.3_IL_1NBS_008_U159_G150UAUG*CUACGtrue98000.31
IL_92114.3_Instance_9 IL_92114.3_IL_1KXK_002_U54_G19UAUGCUAAG
IL_92114.3_Sequence_9 IL_92114.3_IL_1KXK_002_U54_G19UAUG*CUAAGtrue100000.00

Conserved interactions between motif group positions in IL_92114.3:
1 7 s33 
1 9 cWW 
2 4 s35 
2 6 tHW 
2 7 s55 
2 8 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
6 7 s35 
7 8 cSH 
8 9 s35 
7 2 6BPh
JAR3D SCFG/MRF model for IL_92114.3:
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 [9] // Initial node U247 - G227 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012182087,0.013837615,0.014555837,0.036251835,0.000000000],[0.296622029,0.015030447,0.042347731,0.016343772,0.000000000],[0.014885271,0.036529467,0.003301533,0.014494165,0.000000000],[0.042704523,0.014752267,0.412722117,0.013439304,0.000000000],[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 [9] // Basepair U247 - G227 cWW 
ClusterNode  | Deletion Probability [0.0000000006250000] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [8] | Norm Constant [1.000000000000000] // Cluster node A248:A248 and U224:A226
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.024303886,0.050629295,0.005097095,0.592278346,0.000000000],[0.005097095,0.042318173,0.005097095,0.005097095,0.000000000],[0.025002371,0.033833725,0.059652023,0.062880524,0.000000000],[0.005097095,0.005097095,0.023776461,0.054742624,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A248 - U224 tHW 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.410544386,0.302233525,0.014876145,0.012827737,0.000000000],[0.042406868,0.039953161,0.000472966,0.041617784,0.000000000],[0.002226097,0.002186075,0.002779584,0.039725290,0.000000000],[0.006415640,0.041366531,0.000472966,0.039895244,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A225 - A226 cSH 
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 [5] // Initial node U249 - C223 from junction 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.045454545,0.045454545,0.045454545,0.863636364,0.000000000] | Position [1] | Left Index [3] | Right Index [5] // 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 [5] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009540362,0.019435632,0.011046321,0.181049897,0.000000000],[0.016097290,0.007866706,0.194999817,0.012411659,0.000000000],[0.010907271,0.283715261,0.002011465,0.025800426,0.000000000],[0.180004416,0.013028632,0.022255638,0.009829209,0.000000000],[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 G250 - C223 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_92114.3:
> IL_92114.3 IL_1GID_007 U  247 G  227
UAUG*CUAAG
> IL_92114.3 IL_1GID_014 U  247 G  227
UAUG*CUAAG
> IL_92114.3 IL_3T4B_002 U   17 G    6
UAUG*CUAAG
> IL_92114.3 IL_1X8W_007 U  247 G  227
UAUG*CUAAG
> IL_92114.3 IL_1U6B_003 U   80 G   65
UAUG*CUAAG
> IL_92114.3 IL_2Y9B_003 U  846 G  860
UAUG*CUAAG
> IL_92114.3 IL_4FAW_013 U  332 G  350
UAUG*CUAAG
> IL_92114.3 IL_1NBS_008 U  159 G  150
UAUG*CUACG
> IL_92114.3 IL_1KXK_002 U   54 G   19
UAUG*CUAAG