Alignment of IL_25300.3 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_25300.3_Instance_1 IL_25300.3_IL_1KXK_001_U8_G62UAUCGG
IL_25300.3_Sequence_1 IL_25300.3_IL_1KXK_001_U8_G62UAUC*GGtrue74002.44
IL_25300.3_Instance_2 IL_25300.3_IL_2QBG_032_U913_A863UGCGA
IL_25300.3_Sequence_2 IL_25300.3_IL_2QBG_032_U913_A863UGC*GAtrue87001.22
IL_25300.3_Instance_3 IL_25300.3_IL_3V2F_107_C65_G18CAGCG
IL_25300.3_Sequence_3 IL_25300.3_IL_3V2F_107_C65_G18CAG*CGtrue97000.28
IL_25300.3_Instance_4 IL_25300.3_IL_2OZB_001_U24_G48UAGCG
IL_25300.3_Sequence_4 IL_25300.3_IL_2OZB_001_U24_G48UAG*CGtrue100000.00
IL_25300.3_Instance_5 IL_25300.3_IL_3U5H_046_U1015_G1035UCCGUG
IL_25300.3_Sequence_5 IL_25300.3_IL_3U5H_046_U_1015_G_1035UCCG*UGtrue68003.02
IL_25300.3_Instance_6 IL_25300.3_IL_4IOA_024_G938_C864GCGCC
IL_25300.3_Sequence_6 IL_25300.3_IL_4IOA_024_G938_C864GCG*CCtrue98000.23
IL_25300.3_Instance_7 IL_25300.3_IL_4A1B_032_G800_C780GUUAC
IL_25300.3_Sequence_7 IL_25300.3_IL_4A1B_032_G800_C780GUU*ACtrue92000.72

Conserved interactions between motif group positions in IL_25300.3:
1 2 s35 
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35 
JAR3D SCFG/MRF model for IL_25300.3:
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 U8 - G62 from junction 
BasepairNode | Deletion Probability [0.0000000271147100] | Pair Probability [[0.010702699,0.016783297,0.012494699,0.122953415,0.000000000],[0.140350536,0.011316626,0.140267993,0.014057445,0.000000000],[0.012620575,0.147815512,0.002612924,0.020297266,0.000000000],[0.136064500,0.013442467,0.186203276,0.012016769,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.005028411,0.705988837,0.286619400,0.002262785,0.000100568] | Left Letter Distribution [0.318181818,0.318181818,0.136363636,0.227272727,0.000000000] | 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 [4] // Basepair U8 - G62 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.010385667,0.058169139,0.011455548,0.165758616,0.000000000],[0.017993502,0.008638993,0.193985419,0.012726239,0.000000000],[0.011390673,0.204901754,0.002227363,0.077341640,0.000000000],[0.175133380,0.013032785,0.023085878,0.013773406,0.000000000],[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 C11 - G61 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_25300.3:
> IL_25300.3 IL_1KXK_001 U    8 G   62
UAUC*GG
> IL_25300.3 IL_2QBG_032 U  913 A  863
UGC*GA
> IL_25300.3 IL_3V2F_107 C   65 G   18
CAG*CG
> IL_25300.3 IL_2OZB_001 U   24 G   48
UAG*CG
> IL_25300.3 IL_3U5H_046 U 1015 G 1035
UCCG*UG
> IL_25300.3 IL_4IOA_024 G  938 C  864
GCG*CC
> IL_25300.3 IL_4A1B_032 G  800 C  780
GUU*AC