Alignment of IL_62499.7 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
2

2
5
2
I

6
2

3
7
3
I

8
4


9
3
I

10
2

4
11
2
I

12
2

5
13
2
I

14
2

6
15
2
I

16
2

7
17
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_62499.7_Instance_1 IL_62499.7_IL_1FJG_050_G1255_C1282GAUGCUAAUC
IL_62499.7_Sequence_1 IL_62499.7_IL_1FJG_050_G_1255_C_1282GAUG*CUAAUCtrue100000.00
IL_62499.7_Instance_2 IL_62499.7_IL_2AW7_057_G1255_C1282GAAGCGGACC
IL_62499.7_Sequence_2 IL_62499.7_IL_2AW7_057_G_1255_C_1282GAAG*CGGACCtrue92001.20
IL_62499.7_Instance_3 IL_62499.7_IL_3U5F_077_G1488_C1518GUCUAACGUAAUC
IL_62499.7_Sequence_3 IL_62499.7_IL_3U5F_077_G_1488_C_1518GUCUAAC*GUAAUCtrue64005.31

Conserved interactions between motif group positions in IL_62499.7:
1 3 cSS 
1 4 tSS 
1 6 s35 
1 7 cWW 
3 4 cWW 
JAR3D SCFG/MRF model for IL_62499.7:
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 [7] // Initial node G1255 - C1282 from junction 
ClusterNode  | Deletion Probability [0.000000000000000000000000048001338920902248000000000000000000] | Num Left Bases [3] | Num Right Bases [4] | Left Index [1] | Right Index [7] | Norm Constant [0.005026101735550] // Cluster node G1255:G1258 and C1277:C1282
Interaction  | Interacting Bases [1,4] | Pair Probability [[0.011163085,0.013192132,0.019946651,0.012972929,0.000000000],[0.002518887,0.002518887,0.002518887,0.002518887,0.000000000],[0.225176551,0.309004776,0.251654705,0.136738074,0.000000000],[0.002518887,0.002518887,0.002518887,0.002518887,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1255 - C1277 tSS 
Interaction  | Interacting Bases [3,4] | Pair Probability [[0.010041880,0.019391351,0.011641525,0.191240548,0.000000000],[0.018213986,0.008378062,0.218250356,0.013353236,0.000000000],[0.011592485,0.230126887,0.002128781,0.026054525,0.000000000],[0.190871828,0.013570829,0.024804352,0.010339370,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1258 - C1277 cWW 
Interaction  | Interacting Bases [1,7] | Pair Probability [[0.010096111,0.020567805,0.011689796,0.191596493,0.000000000],[0.017034996,0.008324961,0.206359029,0.013134669,0.000000000],[0.011542646,0.241989936,0.002128637,0.027303363,0.000000000],[0.190490110,0.013787581,0.023552083,0.010401784,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1255 - C1282 cWW 
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.045718505,0.071211636,0.067574328,0.059346113,0.000000000],[0.067020919,0.068682141,0.068754223,0.066310020,0.000000000],[0.033617316,0.060370142,0.102093763,0.067927601,0.000000000],[0.066643012,0.022123010,0.068785007,0.063822266,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1255 - G1258 cSS 
Interaction  | Interacting Bases [2,2] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.100000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.300000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1256
Interaction  | Interacting Bases [5,5] | Pair Probability [[0.100000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.500000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion U1278
Interaction  | Interacting Bases [6,6] | Pair Probability [[0.500000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.100000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.300000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.100000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Right strand conserved insertion A1279
Insertion    | Location [2] | Length Distribution [0.010744024,0.644641418,0.010744024,0.005909213,0.322320709,0.005372012,0.000268601] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000]// Insertion after nucleotide 2, position 2 in cluster node
Insertion    | Location [6] | Length Distribution [0.000000000,0.016116035,0.966962127,0.016116035,0.000805802] | Letter Distribution [0.437500000,0.187500000,0.062500000,0.312500000,0.000000000]// Insertion after nucleotide 6, position 6 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 [4] | Right Index [3] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_62499.7:
> IL_62499.7 IL_1FJG_050 G 1255 C 1282
GAUG*CUAAUC
> IL_62499.7 IL_2AW7_057 G 1255 C 1282
GAAG*CGGACC
> IL_62499.7 IL_3U5F_077 G 1488 C 1518
GUCUAAC*GUAAUC