Alignment of IL_46648.6 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
3

3
7
4
I

8
5


9
4
I

10
3

4
11
2
I

12
2

5
13
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_46648.6_Instance_1 IL_46648.6_IL_3V2F_096_C2540_G2523CAAGUG
IL_46648.6_Sequence_1 IL_46648.6_IL_3V2F_096_C_2540_G_2523CAAG*UGtrue100000.00
IL_46648.6_Instance_2 IL_46648.6_IL_2QBG_098_C2540_G2523CAAGUG
IL_46648.6_Sequence_2 IL_46648.6_IL_2QBG_098_C_2540_G_2523CAAG*UGtrue100000.00
IL_46648.6_Instance_3 IL_46648.6_IL_4IOA_093_C2519_G2502CAAGUG
IL_46648.6_Sequence_3 IL_46648.6_IL_4IOA_093_C_2519_G_2502CAAG*UGtrue100000.00
IL_46648.6_Instance_4 IL_46648.6_IL_1S72_087_C2575_G2558CAAGUG
IL_46648.6_Sequence_4 IL_46648.6_IL_1S72_087_C_2575_G_2558CAAG*UGtrue100000.00
IL_46648.6_Instance_5 IL_46648.6_IL_3U5H_117_U2909_A2892UAAGUA
IL_46648.6_Sequence_5 IL_46648.6_IL_3U5H_117_U_2909_A_2892UAAG*UAtrue97000.25
IL_46648.6_Instance_6 IL_46648.6_IL_4A1B_114_A2897_U2880AACGUU
IL_46648.6_Sequence_6 IL_46648.6_IL_4A1B_114_A_2897_U_2880AACG*UUtrue82001.67
IL_46648.6_Instance_7 IL_46648.6_IL_4KQY_004_C73_G50CAAGCG
IL_46648.6_Sequence_7 IL_46648.6_IL_4KQY_004_C73_G50CAAG*CGtrue72002.69
IL_46648.6_Instance_8 IL_46648.6_IL_4LCK_003_G28_C78GAUUAC
IL_46648.6_Sequence_8 IL_46648.6_IL_4LCK_003_G28_C78GAUU*ACtrue56004.16
IL_46648.6_Instance_9 IL_46648.6_IL_3U5H_078_G1776_C1671GUGCC
IL_46648.6_Sequence_9 IL_46648.6_IL_3U5H_078_G_1776_C_1671GUG*CCtrue75002.33
IL_46648.6_Instance_10 IL_46648.6_IL_4C7O_002_A36_U9AUGCU
IL_46648.6_Sequence_10 IL_46648.6_IL_4C7O_002_A36_U9AUG*CUtrue74002.46
IL_46648.6_Instance_11 IL_46648.6_IL_4A1B_069_G1643_C1850GACGC
IL_46648.6_Sequence_11 IL_46648.6_IL_4A1B_069_G_1643_C_1850GAC*GCtrue65003.35
IL_46648.6_Instance_12 IL_46648.6_IL_2QWY_005_C43_G22CUAUG
IL_46648.6_Sequence_12 IL_46648.6_IL_2QWY_005_C43_G22CUA*UGtrue73002.56
IL_46648.6_Instance_13 IL_46648.6_IL_3WBM_004_G2_C24GUAUC
IL_46648.6_Sequence_13 IL_46648.6_IL_3WBM_004_G2_C24GUA*UCtrue72002.64

Conserved interactions between motif group positions in IL_46648.6:
1 2 s35 
1 5 cWW 
2 4 tSH 
3 4 cWW 
4 5 s35 
JAR3D SCFG/MRF model for IL_46648.6:
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 [5] // Initial node C2540 - G2523 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008928161,0.017727990,0.010179535,0.195813486,0.000000000],[0.017922262,0.007857997,0.240697863,0.011633022,0.000000000],[0.010199025,0.222163351,0.001940544,0.023068404,0.000000000],[0.186561134,0.011546440,0.023304029,0.010456756,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.997990020,0.001999980,0.000010000] | Left Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | 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 [5] // Basepair C2540 - G2523 cWW 
ClusterNode  | Deletion Probability [0.0000000047265970] | Num Left Bases [2] | Num Right Bases [1] | Left Index [2] | Right Index [4] | Norm Constant [0.272916602183047] // Cluster node A2541:G2543 and U2522:U2522
Interaction  | Interacting Bases [1,3] | Pair Probability [[0.047861494,0.037204399,0.025318111,0.379123165,0.000000000],[0.020754977,0.013941450,0.003260258,0.003260258,0.000000000],[0.015524934,0.003260258,0.304157596,0.019139174,0.000000000],[0.016587056,0.059970649,0.003260258,0.047375963,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction A2541 - U2522 tSH 
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.011612063,0.139581923,0.011799549,0.134195131,0.000000000],[0.015546252,0.009111562,0.123260216,0.012306578,0.000000000],[0.011634189,0.144484349,0.002483712,0.209875301,0.000000000],[0.121820287,0.013096746,0.018395376,0.020796766,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G2543 - U2522 cWW 
Insertion    | Location [1] | Length Distribution [0.384519277,0.612937839,0.002425294,0.000117590] | Letter Distribution [0.650000000,0.150000000,0.050000000,0.150000000,0.000000000]// Insertion after nucleotide 2, position 1 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_46648.6:
> IL_46648.6 IL_3V2F_096 C 2540 G 2523
CAAG*UG
> IL_46648.6 IL_2QBG_098 C 2540 G 2523
CAAG*UG
> IL_46648.6 IL_4IOA_093 C 2519 G 2502
CAAG*UG
> IL_46648.6 IL_1S72_087 C 2575 G 2558
CAAG*UG
> IL_46648.6 IL_3U5H_117 U 2909 A 2892
UAAG*UA
> IL_46648.6 IL_4A1B_114 A 2897 U 2880
AACG*UU
> IL_46648.6 IL_4KQY_004 C   73 G   50
CAAG*CG
> IL_46648.6 IL_4LCK_003 G   28 C   78
GAUU*AC
> IL_46648.6 IL_3U5H_078 G 1776 C 1671
GUG*CC
> IL_46648.6 IL_4C7O_002 A   36 U    9
AUG*CU
> IL_46648.6 IL_4A1B_069 G 1643 C 1850
GAC*GC
> IL_46648.6 IL_2QWY_005 C   43 G   22
CUA*UG
> IL_46648.6 IL_3WBM_004 G    2 C   24
GUA*UC