Alignment of IL_39980.1 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
5

4
9
6
I

10
7


11
6
I

12
5

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_39980.1_Instance_1 IL_39980.1_IL_4A1B_004_A144_U122AAUUGUAU
IL_39980.1_Sequence_1 IL_39980.1_IL_4A1B_004_A144_U122AAUUGU*AUtrue100000.00
IL_39980.1_Instance_2 IL_39980.1_IL_3U5H_007_A144_U124AGUUGUAU
IL_39980.1_Sequence_2 IL_39980.1_IL_3U5H_007_A144_U124AGUUGU*AUtrue92000.85
IL_39980.1_Instance_3 IL_39980.1_IL_1S72_009_C260_G249CAAUGUAG
IL_39980.1_Sequence_3 IL_39980.1_IL_1S72_009_C260_G249CAAUGU*AGtrue87001.44
IL_39980.1_Instance_4 IL_39980.1_IL_4BPP_061_A1197_U1230AAGGGAUU
IL_39980.1_Sequence_4 IL_39980.1_IL_4BPP_061_A_1197_U_1230AAGGGA*UUtrue86001.47

Conserved interactions between motif group positions in IL_39980.1:
1 2 s35 
1 6 cWW 
3 4 cSH 
4 5 cWW 
4 6 perp 
JAR3D SCFG/MRF model for IL_39980.1:
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 [6] // Initial node A144 - U122 from junction 
BasepairNode | Deletion Probability [0.0000239574126029] | Pair Probability [[0.009264210,0.022192915,0.010074369,0.234029155,0.000000000],[0.019865957,0.008943928,0.203731184,0.010973984,0.000000000],[0.010098514,0.193326205,0.002107237,0.026270642,0.000000000],[0.199529587,0.010865754,0.024111426,0.014614932,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.995990040,0.003999960,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Right Length Distribution [0.995990040,0.003999960,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [1] | Right Index [6] // Basepair A144 - U122 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.583333333,0.083333333,0.250000000,0.083333333,0.000000000] | Position [1] | Left Index [2] | Right Index [5] // Fixed node on left
InitialNode  | Left Length Distribution [0.000000000,0.012187690,0.975015235,0.012187690,0.000609385] | Left Letter Distribution [0.150000000,0.050000000,0.250000000,0.550000000,0.000000000] | Right Length Distribution [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [5] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [3] | Right Index [5] | Norm Constant [0.259243905872397] // Cluster node G148:U149 and A121:A121
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.008973807,0.020802927,0.009627934,0.214768857,0.000000000],[0.022945963,0.009293412,0.189732133,0.010152995,0.000000000],[0.009636163,0.189182448,0.002110966,0.024208445,0.000000000],[0.237966914,0.010117212,0.026275422,0.014204402,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U149 - A121 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.076779974,0.079320859,0.012294084,0.010181688,0.000000000],[0.074799046,0.092378832,0.002581015,0.088429265,0.000000000],[0.192506263,0.010059924,0.020642474,0.156176861,0.000000000],[0.013567760,0.076991426,0.002581015,0.090709515,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G148 - U149 cSH 
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 [5] | Right Index [4] // New Initial node after Cluster
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_39980.1:
> IL_39980.1 IL_4A1B_004 A  144 U  122
AAUUGU*AU
> IL_39980.1 IL_3U5H_007 A  144 U  124
AGUUGU*AU
> IL_39980.1 IL_1S72_009 C  260 G  249
CAAUGU*AG
> IL_39980.1 IL_4BPP_061 A 1197 U 1230
AAGGGA*UU