Alignment of IL_42626.2 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_42626.2_Instance_1 IL_42626.2,IL_4V9F_088,C2547_G2609CCGUCG
IL_42626.2_Sequence_1 IL_42626.24V9F_C_2547_G_2609CC*GUCGtrue88001.16
IL_42626.2_Instance_2 IL_42626.2,IL_8P9A_336,C2881_G2943CUAACG
IL_42626.2_Sequence_2 IL_42626.28P9A_C_2881_G_2943CU*AACGtrue100000.00
IL_42626.2_Instance_3 IL_42626.2,IL_9DFE_105,C2695_G2714CUAUAAG
IL_42626.2_Sequence_3 IL_42626.29DFE_C_2695_G_2714CU*AUAAGtrue64003.46
IL_42626.2_Instance_4 IL_42626.2,IL_8CRE_117,C2853_G2915CUAACG
IL_42626.2_Sequence_4 IL_42626.28CRE_C_2853_G_2915CU*AACGtrue100000.00
IL_42626.2_Instance_5 IL_42626.2,IL_7A0S_097,C2674_G2694CUACAUG
IL_42626.2_Sequence_5 IL_42626.27A0S_C_2674_G_2694CU*ACAUGtrue63003.53
IL_42626.2_Instance_6 IL_42626.2,IL_8CRE_128,C3035_G3052CUAACG
IL_42626.2_Sequence_6 IL_42626.28CRE_C_3035_G_3052CU*AACGtrue100000.00
IL_42626.2_Instance_7 IL_42626.2,IL_3IGI_013,U365_G378UAUACG
IL_42626.2_Sequence_7 IL_42626.23IGI_U365_G378UA*UACGtrue93000.69
IL_42626.2_Instance_8 IL_42626.2,IL_9DFE_098,C2512_G2574CGCACG
IL_42626.2_Sequence_8 IL_42626.29DFE_C_2512_G_2574CG*CACGtrue98000.17
IL_42626.2_Instance_9 IL_42626.2,IL_7A0S_090,C2491_G2553CGCACG
IL_42626.2_Sequence_9 IL_42626.27A0S_C_2491_G_2553CG*CACGtrue98000.17
IL_42626.2_Instance_10 IL_42626.2,IL_5J7L_349,U2695_G2714UUACUG
IL_42626.2_Sequence_10 IL_42626.25J7L_U_2695_G_2714UU*ACUGtrue85001.43
IL_42626.2_Instance_11 IL_42626.2,IL_4WF9_103,U2722_G2741UUAUAG
IL_42626.2_Sequence_11 IL_42626.24WF9_U_2722_G_2741UU*AUAGtrue86001.35
IL_42626.2_Instance_12 IL_42626.2,IL_4WF9_096,C2539_G2601CAUACG
IL_42626.2_Sequence_12 IL_42626.24WF9_C_2539_G_2601CA*UACGtrue98000.17
IL_42626.2_Instance_13 IL_42626.2,IL_5J7L_341,C2512_G2574CAUACG
IL_42626.2_Sequence_13 IL_42626.25J7L_C_2512_G_2574CA*UACGtrue98000.17
IL_42626.2_Instance_14 IL_42626.2,IL_1KXK_003,U28_G45UGCACG
IL_42626.2_Sequence_14 IL_42626.21KXK_U28_G45UG*CACGtrue93000.70

Conserved interactions between motif group positions in IL_42626.2:
1 2 s35 
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35
JAR3D SCFG/MRF model for IL_42626.2:
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 [4] // Initial node
BasepairNode | Deletion Probability [0.0000000002895327] | Pair Probability [[0.008969761,0.014504301,0.010656642,0.136574671,0.000000000],[0.090299181,0.013352686,0.232102407,0.012912518,0.000000000],[0.010815234,0.139273999,0.002180738,0.018747938,0.000000000],[0.150727103,0.012244267,0.136715226,0.009923328,0.000000000],[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 [0.000000000,0.003038975,0.851419455,0.144857801,0.000658445,0.000025325] | Right Letter Distribution [0.421875000,0.390625000,0.015625000,0.171875000,0.000000000] | Left Index [1] | Right Index [4] // Basepair C2547 - G2609 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008297200,0.017048681,0.009160150,0.204582216,0.000000000],[0.017794466,0.008685966,0.186404359,0.010355522,0.000000000],[0.009149365,0.204057250,0.001840014,0.027144774,0.000000000],[0.241414653,0.010248314,0.034463575,0.009353495,0.000000000],[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 C2548 - G2606 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_42626.2:
> IL_42626.2  4V9F C 2547 G 2609
CC*GUCG
> IL_42626.2  8P9A C 2881 G 2943
CU*AACG
> IL_42626.2  9DFE C 2695 G 2714
CU*AUAAG
> IL_42626.2  8CRE C 2853 G 2915
CU*AACG
> IL_42626.2  7A0S C 2674 G 2694
CU*ACAUG
> IL_42626.2  8CRE C 3035 G 3052
CU*AACG
> IL_42626.2  3IGI U  365 G  378
UA*UACG
> IL_42626.2  9DFE C 2512 G 2574
CG*CACG
> IL_42626.2  7A0S C 2491 G 2553
CG*CACG
> IL_42626.2  5J7L U 2695 G 2714
UU*ACUG
> IL_42626.2  4WF9 U 2722 G 2741
UU*AUAG
> IL_42626.2  4WF9 C 2539 G 2601
CA*UACG
> IL_42626.2  5J7L C 2512 G 2574
CA*UACG
> IL_42626.2  1KXK U   28 G   45
UG*CACG