Alignment of IL_73000.2 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


7
4
I

8
3

3
9
3
I

10
3

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_73000.2_Instance_1 IL_73000.2_IL_3UCZ_004_G76_C64GUAAAC
IL_73000.2_Sequence_1 IL_73000.2_IL_3UCZ_004_G76_C64GU*AAACtrue100000.00
IL_73000.2_Instance_2 IL_73000.2_IL_3IWN_005_G71_C54GUAAAC
IL_73000.2_Sequence_2 IL_73000.2_IL_3IWN_005_G71_C54GU*AAACtrue100000.00
IL_73000.2_Instance_3 IL_73000.2_IL_2AW7_054_G1142_C1132GGCAGC
IL_73000.2_Sequence_3 IL_73000.2_IL_2AW7_054_G_1142_C_1132GG*CAGCtrue94000.60
IL_73000.2_Instance_4 IL_73000.2_IL_2AW7_013_G213_C206GCGGAC
IL_73000.2_Sequence_4 IL_73000.2_IL_2AW7_013_G213_C206GC*GGACtrue92000.79
IL_73000.2_Instance_5 IL_73000.2_IL_4A1B_066_G1539_C1531GUUAGAAC
IL_73000.2_Sequence_5 IL_73000.2_IL_4A1B_066_G_1539_C_1531GUU*AGAACtrue60003.76
IL_73000.2_Instance_6 IL_73000.2_IL_2QBG_003_C30_G54CCGAAG
IL_73000.2_Sequence_6 IL_73000.2_IL_2QBG_003_C30_G54CC*GAAGtrue93000.67
IL_73000.2_Instance_7 IL_73000.2_IL_2AW7_044_G933_C1384GCAUUCCC
IL_73000.2_Sequence_7 IL_73000.2_IL_2AW7_044_G933_C_1384GCA*UUCCCtrue44005.32

Conserved interactions between motif group positions in IL_73000.2:
1 2 s35 
1 6 cWW 
2 3 cWW 
2 5 cSW 
3 4 cSH 
4 5 s35 
5 6 s35 
JAR3D SCFG/MRF model for IL_73000.2:
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 [6] // Initial node G76 - C64 from junction 
BasepairNode | Deletion Probability [0.0000052393233623] | Pair Probability [[0.009696313,0.019313569,0.011232880,0.184287162,0.000000000],[0.016884566,0.008035654,0.208890895,0.012733823,0.000000000],[0.011131706,0.260092205,0.002049121,0.025767468,0.000000000],[0.183526462,0.013182737,0.023188255,0.009987184,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | 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 [6] // Basepair G76 - C64 cWW 
ClusterNode  | Deletion Probability [0.0000000001323925] | Num Left Bases [1] | Num Right Bases [3] | Left Index [2] | Right Index [5] | Norm Constant [0.062935737109612] // Cluster node U77:U77 and A61:A63
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.009104522,0.019068653,0.010130221,0.202038967,0.000000000],[0.020744927,0.008639905,0.211004470,0.011238095,0.000000000],[0.010155036,0.200458510,0.002050733,0.023679133,0.000000000],[0.223086224,0.011128398,0.025343219,0.012128987,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U77 - A61 cWW 
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.126758533,0.055585452,0.014037661,0.008663852,0.000000000],[0.168755935,0.040188393,0.013939587,0.009789708,0.000000000],[0.117302516,0.039733096,0.144249774,0.007108942,0.000000000],[0.194184319,0.042380809,0.009741284,0.007580138,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U77 - A63 cSW 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.119225934,0.088672012,0.046358530,0.009822107,0.000000000],[0.098358845,0.084485776,0.002105316,0.085313352,0.000000000],[0.092777380,0.010484959,0.066131830,0.084785516,0.000000000],[0.029200906,0.097227503,0.002105316,0.082944717,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A61 - A62 cSH 
Insertion    | Location [2] | Length Distribution [0.709556780,0.288067923,0.002274220,0.000101076] | Letter Distribution [0.125000000,0.125000000,0.375000000,0.375000000,0.000000000]// Insertion after nucleotide 3, position 2 in cluster node
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 [3] | Right Index [2] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [3] | Right Index [3] | 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_73000.2:
> IL_73000.2 IL_3UCZ_004 G   76 C   64
GU*AAAC
> IL_73000.2 IL_3IWN_005 G   71 C   54
GU*AAAC
> IL_73000.2 IL_2AW7_054 G 1142 C 1132
GG*CAGC
> IL_73000.2 IL_2AW7_013 G  213 C  206
GC*GGAC
> IL_73000.2 IL_4A1B_066 G 1539 C 1531
GUU*AGAAC
> IL_73000.2 IL_2QBG_003 C   30 G   54
CC*GAAG
> IL_73000.2 IL_2AW7_044 G  933 C 1384
GCA*UUCCC