Alignment of IL_07039.3 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
4
I

6
5

3
7
5
I

8
6


9
5
I

10
5

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_07039.3_Instance_1 IL_07039.3,IL_4V9F_086,U2615_G2543UGGCG
IL_07039.3_Sequence_1 IL_07039.34V9F_U_2615_G_2543UGG*CGtrue100000.00
IL_07039.3_Instance_2 IL_07039.3,IL_8P9A_334,U2949_G2877UGGCG
IL_07039.3_Sequence_2 IL_07039.38P9A_U_2949_G_2877UGG*CGtrue100000.00
IL_07039.3_Instance_3 IL_07039.3,IL_8CRE_115,U2921_G2849UGGCG
IL_07039.3_Sequence_3 IL_07039.38CRE_U_2921_G_2849UGG*CGtrue100000.00
IL_07039.3_Instance_4 IL_07039.3,IL_4WF9_094,U2607_G2535UGGCG
IL_07039.3_Sequence_4 IL_07039.34WF9_U_2607_G_2535UGG*CGtrue100000.00
IL_07039.3_Instance_5 IL_07039.3,IL_9DFE_096,U2580_G2508UGGCG
IL_07039.3_Sequence_5 IL_07039.39DFE_U_2580_G_2508UGG*CGtrue100000.00
IL_07039.3_Instance_6 IL_07039.3,IL_7A0S_088,U2559_G2487UGGCG
IL_07039.3_Sequence_6 IL_07039.37A0S_U_2559_G_2487UGG*CGtrue100000.00
IL_07039.3_Instance_7 IL_07039.3,IL_4V9F_083,U2492_G2529UCGUG
IL_07039.3_Sequence_7 IL_07039.34V9F_U_2492_G_2529UCG*UGtrue79002.50
IL_07039.3_Instance_8 IL_07039.3,IL_8CRE_112,U2798_G2835UUGUG
IL_07039.3_Sequence_8 IL_07039.38CRE_U_2798_G_2835UUG*UGtrue84001.99
IL_07039.3_Instance_9 IL_07039.3,IL_8P9A_331,U2826_G2863UUGUG
IL_07039.3_Sequence_9 IL_07039.38P9A_U_2826_G_2863UUG*UGtrue84001.99
IL_07039.3_Instance_10 IL_07039.3,IL_5J7L_394,U2580_G2508UGGCG
IL_07039.3_Sequence_10 IL_07039.35J7L_U_2580_G_2508UGG*CGtrue100000.00
IL_07039.3_Instance_11 IL_07039.3,IL_5J7L_393,U2457_G2494UGAUG
IL_07039.3_Sequence_11 IL_07039.35J7L_U_2457_G_2494UGA*UGtrue98000.25
IL_07039.3_Instance_12 IL_07039.3,IL_5XTM_004,U3_G45UAUAG
IL_07039.3_Sequence_12 IL_07039.35XTM_U3_G45UAU*AGtrue96000.53
IL_07039.3_Instance_13 IL_07039.3,IL_5DCV_005,U3_G49UAUAG
IL_07039.3_Sequence_13 IL_07039.35DCV_U3_G49UAU*AGtrue96000.53
IL_07039.3_Instance_14 IL_07039.3,IL_1U6B_010,U160_G151UAUAG
IL_07039.3_Sequence_14 IL_07039.31U6B_U160_G151UAU*AGtrue96000.53
IL_07039.3_Instance_15 IL_07039.3,IL_5VCI_004,U2_G12UAUAG
IL_07039.3_Sequence_15 IL_07039.35VCI_U2_G12UAU*AGtrue96000.53
IL_07039.3_Instance_16 IL_07039.3,IL_4PCJ_004,U25_G12UAUAG
IL_07039.3_Sequence_16 IL_07039.34PCJ_U25_G12UAU*AGtrue96000.53

Conserved interactions between motif group positions in IL_07039.3:
1 2 s33 
1 5 cWW 
3 4 cWW 
3 5 s55 
4 5 s35
JAR3D SCFG/MRF model for IL_07039.3:
Character Definition | A,C,G,U,* // Identity and order of characters in matrices
InitialNode  | Left Length Distribution [0.999900000,0.000100000] | Left Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Right Length Distribution [0.999900000,0.000100000] | Right Letter Distribution [0.000000000,0.000000000,0.000000000,0.000000000,0.000000000] | Left Index [1] | Right Index [5] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009888854,0.012296250,0.012554439,0.032775936,0.000000000],[0.266024927,0.024577378,0.037242412,0.014098979,0.000000000],[0.012829285,0.032644651,0.002907130,0.012901250,0.000000000],[0.075790235,0.012907528,0.428644021,0.011916725,0.000000000],[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 U2615 - G2543 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.305555556,0.083333333,0.472222222,0.138888889,0.000000000] | Position [1] | Left Index [2] | Right Index [4] // Fixed node on left for 4V9F|1|0|G|2543
InitialNode  | 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 [1.000000000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [3] | Right Index [4] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.009348713,0.062777142,0.009892584,0.165177206,0.000000000],[0.015859938,0.009008582,0.148908805,0.011089544,0.000000000],[0.009798910,0.211815470,0.002012551,0.098906659,0.000000000],[0.192536373,0.011355053,0.027308377,0.014204094,0.000000000],[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 [3] | Right Index [4] // Basepair G2617 - C2542 cWW 
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_07039.3:
> IL_07039.3  4V9F U 2615 G 2543
UGG*CG
> IL_07039.3  8P9A U 2949 G 2877
UGG*CG
> IL_07039.3  8CRE U 2921 G 2849
UGG*CG
> IL_07039.3  4WF9 U 2607 G 2535
UGG*CG
> IL_07039.3  9DFE U 2580 G 2508
UGG*CG
> IL_07039.3  7A0S U 2559 G 2487
UGG*CG
> IL_07039.3  4V9F U 2492 G 2529
UCG*UG
> IL_07039.3  8CRE U 2798 G 2835
UUG*UG
> IL_07039.3  8P9A U 2826 G 2863
UUG*UG
> IL_07039.3  5J7L U 2580 G 2508
UGG*CG
> IL_07039.3  5J7L U 2457 G 2494
UGA*UG
> IL_07039.3  5XTM U    3 G   45
UAU*AG
> IL_07039.3  5DCV U    3 G   49
UAU*AG
> IL_07039.3  1U6B U  160 G  151
UAU*AG
> IL_07039.3  5VCI U    2 G   12
UAU*AG
> IL_07039.3  4PCJ U   25 G   12
UAU*AG