Alignment of IL_64231.5 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

3
7
5
I

8
6

4
9
7
I

10
10

5
11
10
I

12
11


13
10
I

14
10

6
15
9
I

16
8

7
17
3
I

18
3

8
19
2
I

20
2

9
21
1
I


In
acceptance
region

Cutoff
score
Full
edit
distance
Interior
edit
distance
Alignment
score
deficit
IL_64231.5_Instance_1 IL_64231.5,IL_4LFB_008,C132_G230CUACCGAUG
IL_64231.5_Sequence_1 IL_64231.54LFB_C132_G230CUACC*GAUGtrue99000.14
IL_64231.5_Instance_2 IL_64231.5,IL_5J7L_010,C132_G230CUGCCGAUG
IL_64231.5_Sequence_2 IL_64231.55J7L_C132_G230CUGCC*GAUGtrue81001.88
IL_64231.5_Instance_3 IL_64231.5,IL_3BNT_002,G14_C9GCAAGCACC
IL_64231.5_Sequence_3 IL_64231.53BNT_G14_C9GCAAG*CACCtrue90000.96
IL_64231.5_Instance_4 IL_64231.5,IL_3BNR_008,G13_C10GCAAGCACC
IL_64231.5_Sequence_4 IL_64231.53BNR_G13_C10GCAAG*CACCtrue90000.96
IL_64231.5_Instance_5 IL_64231.5,IL_3LOA_001,G1497_C1404GUAACGCCC
IL_64231.5_Sequence_5 IL_64231.53LOA_G_1497_C_1404GUAAC*GCCCtrue79002.05
IL_64231.5_Instance_6 IL_64231.5,IL_2O3V_002,A38_U10AAAAGCGCU
IL_64231.5_Sequence_6 IL_64231.52O3V_A38_U10AAAAG*CGCUtrue96000.41
IL_64231.5_Instance_7 IL_64231.5,IL_5J7L_353,C2870_G2846CUAACGGUG
IL_64231.5_Sequence_7 IL_64231.55J7L_C_2870_G_2846CUAAC*GGUGtrue100000.00
IL_64231.5_Instance_8 IL_64231.5,IL_8VMA_001,C22_G19CCCACGUUG
IL_64231.5_Sequence_8 IL_64231.58VMA_C22_G19CCCAC*GUUGtrue61003.79
IL_64231.5_Instance_9 IL_64231.5,IL_1HYS_004,U880_A874UUUCUGAAA
IL_64231.5_Sequence_9 IL_64231.51HYS_U880_A874UUUCU*GAAAtrue50004.94
IL_64231.5_Instance_10 IL_64231.5,IL_1U6B_004,C96_G122CAAGCGAAG
IL_64231.5_Sequence_10 IL_64231.51U6B_C96_G122CAAGC*GAAGtrue70002.91
IL_64231.5_Instance_11 IL_64231.5,IL_8P9A_455,A1753_U1647AAAAGCGCU
IL_64231.5_Sequence_11 IL_64231.58P9A_A_1753_U_1647AAAAG*CGCUtrue96000.41

Conserved interactions between motif group positions in IL_64231.5:
1 2 s35 
1 9 cWW 
2 8 cWW 
3 4 s35 
4 5 s35 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35
JAR3D SCFG/MRF model for IL_64231.5:
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 [9] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008728406,0.017366575,0.009841489,0.202007349,0.000000000],[0.017522511,0.008870945,0.232109437,0.011742763,0.000000000],[0.009860457,0.213314839,0.001908274,0.027325445,0.000000000],[0.192754133,0.011714420,0.025358709,0.009574247,0.000000000],[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 [9] // Basepair C132 - G230 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.034971441,0.198541300,0.015167725,0.045169145,0.000000000],[0.014394190,0.058395545,0.043491498,0.071434667,0.000000000],[0.015360301,0.043809855,0.003040448,0.067116055,0.000000000],[0.053281350,0.077909383,0.019263841,0.238653256,0.000000000],[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 [2] | Right Index [8] // Basepair U133 - U229 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.653846154,0.115384615,0.115384615,0.115384615,0.000000000] | Position [1] | Left Index [3] | Right Index [7] // Fixed node on left for 4LFB|1|A|A|134
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 [4] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.576923077,0.269230769,0.115384615,0.038461538,0.000000000] | Position [1] | Left Index [4] | Right Index [7] // Fixed node on left for 4LFB|1|A|C|135
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 [5] | Right Index [7] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.500000000,0.115384615,0.269230769,0.115384615,0.000000000] | Position [2] | Left Index [5] | Right Index [7] // Fixed node on right for 4LFB|1|A|A|228
InitialNode  | Left Length Distribution [1.000000000] | 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 [5] | Right Index [6] // New Initial node after Fixed node
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008972022,0.016513759,0.010391698,0.170024537,0.000000000],[0.041149734,0.010392686,0.230178514,0.012690603,0.000000000],[0.010438389,0.210737037,0.002021772,0.021931248,0.000000000],[0.174541840,0.012493228,0.057885954,0.009636978,0.000000000],[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 [5] | Right Index [6] // Basepair C136 - G227 cWW 
HairpinNode  | Num Bases [1] | Left Index [6] | Right Index [6] | 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_64231.5:
> IL_64231.5  4LFB C  132 G  230
CUACC*GAUG
> IL_64231.5  5J7L C  132 G  230
CUGCC*GAUG
> IL_64231.5  3BNT G   14 C    9
GCAAG*CACC
> IL_64231.5  3BNR G   13 C   10
GCAAG*CACC
> IL_64231.5  3LOA G 1497 C 1404
GUAAC*GCCC
> IL_64231.5  2O3V A   38 U   10
AAAAG*CGCU
> IL_64231.5  5J7L C 2870 G 2846
CUAAC*GGUG
> IL_64231.5  8VMA C   22 G   19
CCCAC*GUUG
> IL_64231.5  1HYS U  880 A  874
UUUCU*GAAA
> IL_64231.5  1U6B C   96 G  122
CAAGC*GAAG
> IL_64231.5  8P9A A 1753 U 1647
AAAAG*CGCU