Alignment of IL_13069.3 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
3
I

6
4


7
3
I

8
3

3
9
2
I

10
2

4
11
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_13069.3_Instance_1 IL_13069.3_IL_2QBG_026_G775_C791GGGCAAUC
IL_13069.3_Sequence_1 IL_13069.3_IL_2QBG_026_G775_C791GGG*CAAUCtrue100000.00
IL_13069.3_Instance_2 IL_13069.3_IL_3V2F_023_G775_C791GGAUAACC
IL_13069.3_Sequence_2 IL_13069.3_IL_3V2F_023_G775_C791GGA*UAACCtrue98000.25
IL_13069.3_Instance_3 IL_13069.3_IL_1S72_031_G868_C884GGGCCAUC
IL_13069.3_Sequence_3 IL_13069.3_IL_1S72_031_G868_C884GGG*CCAUCtrue88001.19
IL_13069.3_Instance_4 IL_13069.3_IL_4IOA_020_G788_C804GGAUAACC
IL_13069.3_Sequence_4 IL_13069.3_IL_4IOA_020_G788_C804GGA*UAACCtrue98000.25
IL_13069.3_Instance_5 IL_13069.3_IL_3U5H_035_G907_C923GGGUAAUC
IL_13069.3_Sequence_5 IL_13069.3_IL_3U5H_035_G907_C923GGG*UAAUCtrue99000.11
IL_13069.3_Instance_6 IL_13069.3_IL_4A1B_040_G932_C948GGGUAAUC
IL_13069.3_Sequence_6 IL_13069.3_IL_4A1B_040_G932_C948GGG*UAAUCtrue99000.11

Conserved interactions between motif group positions in IL_13069.3:
1 2 s55 
1 3 s53 
1 4 cWW 
2 3 cWW 
3 4 s33 
JAR3D SCFG/MRF model for IL_13069.3:
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 [4] // Initial node G775 - C791 from junction 
BasepairNode | Deletion Probability [0.0000000000000155] | Pair Probability [[0.009810372,0.019985697,0.011358953,0.186173951,0.000000000],[0.016552873,0.008089349,0.200518679,0.012762933,0.000000000],[0.011215968,0.263443051,0.002068393,0.026530626,0.000000000],[0.185098881,0.013397366,0.022885515,0.010107394,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.008193363,0.983203605,0.008193363,0.000409668] | Left Letter Distribution [0.062500000,0.062500000,0.812500000,0.062500000,0.000000000] | Right Length Distribution [0.000000000,0.000000000,0.008193363,0.983203605,0.008193363,0.000409668] | Right Letter Distribution [0.575000000,0.175000000,0.025000000,0.225000000,0.000000000] | Left Index [1] | Right Index [4] // Basepair G775 - C791 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.011529978,0.114026310,0.011927368,0.164155828,0.000000000],[0.016602246,0.009385099,0.140755504,0.012500592,0.000000000],[0.011763808,0.164040638,0.002486250,0.147401099,0.000000000],[0.140179758,0.013269385,0.020057334,0.019918804,0.000000000],[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 [2] | Right Index [3] // Basepair G777 - C787 cWW 
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_13069.3:
> IL_13069.3 IL_2QBG_026 G  775 C  791
GGG*CAAUC
> IL_13069.3 IL_3V2F_023 G  775 C  791
GGA*UAACC
> IL_13069.3 IL_1S72_031 G  868 C  884
GGG*CCAUC
> IL_13069.3 IL_4IOA_020 G  788 C  804
GGA*UAACC
> IL_13069.3 IL_3U5H_035 G  907 C  923
GGG*UAAUC
> IL_13069.3 IL_4A1B_040 G  932 C  948
GGG*UAAUC