Alignment of IL_92109.3 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
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_92109.3_Instance_1 IL_92109.3_IL_1S72_086_C2547_G2609CCGUCG
IL_92109.3_Sequence_1 IL_92109.3_IL_1S72_086_C_2547_G_2609CC*GUCGtrue83001.63
IL_92109.3_Instance_2 IL_92109.3_IL_3U5H_115_C2881_G2943CUAACG
IL_92109.3_Sequence_2 IL_92109.3_IL_3U5H_115_C_2881_G_2943CU*AACGtrue84001.51
IL_92109.3_Instance_3 IL_92109.3_IL_4A1B_113_C2869_G2931CUAACG
IL_92109.3_Sequence_3 IL_92109.3_IL_4A1B_113_C_2869_G_2931CU*AACGtrue84001.51
IL_92109.3_Instance_4 IL_92109.3_IL_4IOA_099_C2674_G2694CUACAUG
IL_92109.3_Sequence_4 IL_92109.3_IL_4IOA_099_C_2674_G_2694CU*ACAUGtrue52004.53
IL_92109.3_Instance_5 IL_92109.3_IL_3V2F_095_C2512_G2574CGCACG
IL_92109.3_Sequence_5 IL_92109.3_IL_3V2F_095_C_2512_G_2574CG*CACGtrue84001.53
IL_92109.3_Instance_6 IL_92109.3_IL_4IOA_092_C2491_G2553CGCACG
IL_92109.3_Sequence_6 IL_92109.3_IL_4IOA_092_C_2491_G_2553CG*CACGtrue84001.53
IL_92109.3_Instance_7 IL_92109.3_IL_2QBG_022_G697_C765GCGAC
IL_92109.3_Sequence_7 IL_92109.3_IL_2QBG_022_G697_C765GC*GACtrue100000.00
IL_92109.3_Instance_8 IL_92109.3_IL_3U5H_031_G833_C861GUGGC
IL_92109.3_Sequence_8 IL_92109.3_IL_3U5H_031_G833_C861GU*GGCtrue61003.75
IL_92109.3_Instance_9 IL_92109.3_IL_3SNP_002_A13_U20ACGUU
IL_92109.3_Sequence_9 IL_92109.3_IL_3SNP_002_A13_U20AC*GUUtrue94000.57
IL_92109.3_Instance_10 IL_92109.3_IL_3SN2_002_G13_C20GCGCC
IL_92109.3_Sequence_10 IL_92109.3_IL_3SN2_002_G13_C20GC*GCCtrue95000.46
IL_92109.3_Instance_11 IL_92109.3_IL_3V2F_008_G271I_C271OGCGUC
IL_92109.3_Sequence_11 IL_92109.3_IL_3V2F_008_G_271I_C_271OGC*GUCtrue96000.35
IL_92109.3_Instance_12 IL_92109.3_IL_2QBG_097_C2512_G2574CAUACG
IL_92109.3_Sequence_12 IL_92109.3_IL_2QBG_097_C_2512_G_2574CA*UACGtrue83001.62
IL_92109.3_Instance_13 IL_92109.3_IL_4BPP_033_U1076_A616UCGUUAAAA
IL_92109.3_Sequence_13 IL_92109.3_IL_4BPP_033_U_1076_A616UC*GUUAAAAtrue42005.55
IL_92109.3_Instance_14 IL_92109.3_IL_4OO8_002_G54_C60GCGUC
IL_92109.3_Sequence_14 IL_92109.3_IL_4OO8_002_G54_C60GC*GUCtrue96000.35
IL_92109.3_Instance_15 IL_92109.3_IL_3U5F_033_U1104_A622UCGUUAAAA
IL_92109.3_Sequence_15 IL_92109.3_IL_3U5F_033_U_1104_A622UC*GUUAAAAtrue42005.55

Conserved interactions between motif group positions in IL_92109.3:
1 2 s35 
1 4 cWW 
2 3 cWW 
2 4 s55 
3 4 s35 
JAR3D SCFG/MRF model for IL_92109.3:
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 [4] // Initial node C2547 - G2609 from junction 
BasepairNode | Deletion Probability [0.0000000004335789] | Pair Probability [[0.008791164,0.017088285,0.010056729,0.182749433,0.000000000],[0.017769220,0.007709097,0.245759773,0.011520229,0.000000000],[0.010075308,0.227524758,0.001907120,0.022437230,0.000000000],[0.192056308,0.011437882,0.023135090,0.009982373,0.000000000],[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 [0.001324284,0.398609502,0.398830216,0.067604701,0.000728356,0.132439442,0.000441428,0.000022071] | Right Letter Distribution [0.409090909,0.257575758,0.045454545,0.287878788,0.000000000] | Left Index [1] | Right Index [4] // Basepair C2547 - G2609 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008884572,0.016486355,0.010152446,0.174353499,0.000000000],[0.036137873,0.008237886,0.244341815,0.011637174,0.000000000],[0.010227979,0.189336687,0.001988916,0.021267196,0.000000000],[0.193505768,0.011294003,0.051751617,0.010396213,0.000000000],[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_92109.3:
> IL_92109.3 IL_1S72_086 C 2547 G 2609
CC*GUCG
> IL_92109.3 IL_3U5H_115 C 2881 G 2943
CU*AACG
> IL_92109.3 IL_4A1B_113 C 2869 G 2931
CU*AACG
> IL_92109.3 IL_4IOA_099 C 2674 G 2694
CU*ACAUG
> IL_92109.3 IL_3V2F_095 C 2512 G 2574
CG*CACG
> IL_92109.3 IL_4IOA_092 C 2491 G 2553
CG*CACG
> IL_92109.3 IL_2QBG_022 G  697 C  765
GC*GAC
> IL_92109.3 IL_3U5H_031 G  833 C  861
GU*GGC
> IL_92109.3 IL_3SNP_002 A   13 U   20
AC*GUU
> IL_92109.3 IL_3SN2_002 G   13 C   20
GC*GCC
> IL_92109.3 IL_3V2F_008 G 271I C 271O
GC*GUC
> IL_92109.3 IL_2QBG_097 C 2512 G 2574
CA*UACG
> IL_92109.3 IL_4BPP_033 U 1076 A  616
UC*GUUAAAA
> IL_92109.3 IL_4OO8_002 G   54 C   60
GC*GUC
> IL_92109.3 IL_3U5F_033 U 1104 A  622
UC*GUUAAAA