Alignment of IL_24546.4 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
6
I

8
7

4
9
8
I

10
9

5
11
9
I

12
9

6
13
9
I

14
9

7
15
9
I

16
9

8
17
10
I

18
11


19
10
I

20
9

9
21
2
I

22
2

10
23
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_24546.4_Instance_1 IL_24546.4_IL_3V2F_037_C1004_G1151CCCCCAAGCG
IL_24546.4_Sequence_1 IL_24546.4_IL_3V2F_037_C_1004_G_1151CCCCCAAG*CGtrue98000.26
IL_24546.4_Instance_2 IL_24546.4_IL_4IOA_033_U1015_A1162UCCCUAAAUA
IL_24546.4_Sequence_2 IL_24546.4_IL_4IOA_033_U_1015_A_1162UCCCUAAA*UAtrue91001.18
IL_24546.4_Instance_3 IL_24546.4_IL_2QBG_037_U1004_A1151UCCCAAAGCA
IL_24546.4_Sequence_3 IL_24546.4_IL_2QBG_037_U_1004_A_1151UCCCAAAG*CAtrue95000.65
IL_24546.4_Instance_4 IL_24546.4_IL_1S72_039_U1101_A1255UCCCCAAGCA
IL_24546.4_Sequence_4 IL_24546.4_IL_1S72_039_U_1101_A_1255UCCCCAAG*CAtrue98000.24
IL_24546.4_Instance_5 IL_24546.4_IL_4A1B_055_C1200_G1353CGCCCAAAUG
IL_24546.4_Sequence_5 IL_24546.4_IL_4A1B_055_C_1200_G_1353CGCCCAAA*UGtrue100000.00
IL_24546.4_Instance_6 IL_24546.4_IL_2AW7_027_C504_G541CGGCUAACGG
IL_24546.4_Sequence_6 IL_24546.4_IL_2AW7_027_C504_G541CGGCUAAC*GGtrue91001.21
IL_24546.4_Instance_7 IL_24546.4_IL_4BPP_029_A543_U582AGGGCAAGCU
IL_24546.4_Sequence_7 IL_24546.4_IL_4BPP_029_A543_U582AGGGCAAG*CUtrue89001.56
IL_24546.4_Instance_8 IL_24546.4_IL_1FJG_020_C504_G541CGGCCAACGG
IL_24546.4_Sequence_8 IL_24546.4_IL_1FJG_020_C504_G541CGGCCAAC*GGtrue97000.39
IL_24546.4_Instance_9 IL_24546.4_IL_3U5F_030_A550_U588AGGGCAAGCU
IL_24546.4_Sequence_9 IL_24546.4_IL_3U5F_030_A550_U588AGGGCAAG*CUtrue89001.56
IL_24546.4_Instance_10 IL_24546.4_IL_3U5H_054_U1173_A1326UGCCGGAAUA
IL_24546.4_Sequence_10 IL_24546.4_IL_3U5H_054_U_1173_A_1326UGCCGGAA*UAtrue89001.54

Conserved interactions between motif group positions in IL_24546.4:
1 8 s35 
1 10 cWW 
2 3 s35 
3 4 s35 
4 5 s33 
5 6 cSH 
6 7 s35 
8 9 cWW 
8 10 s55 
9 10 s35 
JAR3D SCFG/MRF model for IL_24546.4:
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 [10] // Initial node C1004 - G1151 from junction 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008817364,0.018381954,0.009785358,0.206269672,0.000000000],[0.020516944,0.008438985,0.223661289,0.010919998,0.000000000],[0.009843600,0.184652701,0.001994662,0.022747658,0.000000000],[0.226368298,0.010661853,0.024935691,0.012003973,0.000000000],[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 [10] // Basepair C1004 - G1151 cWW 
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.375000000,0.541666667,0.041666667,0.000000000] | Position [1] | Left Index [2] | Right Index [9] // Fixed node on left
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.541666667,0.375000000,0.041666667,0.000000000] | Position [1] | Left Index [3] | Right Index [9] // Fixed node on left
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 [9] // New Initial node after Fixed node
FixedNode    | Deletion Probability [0.0050000000000000] | Letter Distribution [0.041666667,0.708333333,0.208333333,0.041666667,0.000000000] | Position [1] | Left Index [4] | Right Index [9] // Fixed node on left
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 [9] // New Initial node after Fixed node
ClusterNode  | Deletion Probability [0.0000000000031250] | Num Left Bases [4] | Num Right Bases [1] | Left Index [5] | Right Index [9] | Norm Constant [0.999999999999999] // Cluster node C1008:G1011 and C1150:C1150
Interaction  | Interacting Bases [4,5] | Pair Probability [[0.009160501,0.019617847,0.010363923,0.212411613,0.000000000],[0.017414703,0.008074462,0.208142248,0.011590854,0.000000000],[0.010317943,0.237552545,0.001992866,0.024923795,0.000000000],[0.182586497,0.011794457,0.022702265,0.011353480,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G1011 - C1150 cWW 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.108026987,0.108970689,0.008009132,0.006289163,0.000000000],[0.162368586,0.088700096,0.001351892,0.090898797,0.000000000],[0.006358471,0.028715989,0.034561486,0.088161796,0.000000000],[0.071026857,0.108115302,0.001351892,0.087092865,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction C1008 - A1009 cSH 
Interaction  | Interacting Bases [3,3] | Pair Probability [[0.875000000,0.000000000,0.000000000,0.000000000,0.000000000],[0.000000000,0.041666667,0.000000000,0.000000000,0.000000000],[0.000000000,0.000000000,0.041666667,0.000000000,0.000000000],[0.000000000,0.000000000,0.000000000,0.041666667,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Left strand conserved insertion A1010
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 [9] | Right Index [8] // New Initial node after Cluster
HairpinNode  | Num Bases [1] | Left Index [9] | Right Index [9] | 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_24546.4:
> IL_24546.4 IL_3V2F_037 C 1004 G 1151
CCCCCAAG*CG
> IL_24546.4 IL_4IOA_033 U 1015 A 1162
UCCCUAAA*UA
> IL_24546.4 IL_2QBG_037 U 1004 A 1151
UCCCAAAG*CA
> IL_24546.4 IL_1S72_039 U 1101 A 1255
UCCCCAAG*CA
> IL_24546.4 IL_4A1B_055 C 1200 G 1353
CGCCCAAA*UG
> IL_24546.4 IL_2AW7_027 C  504 G  541
CGGCUAAC*GG
> IL_24546.4 IL_4BPP_029 A  543 U  582
AGGGCAAG*CU
> IL_24546.4 IL_1FJG_020 C  504 G  541
CGGCCAAC*GG
> IL_24546.4 IL_3U5F_030 A  550 U  588
AGGGCAAG*CU
> IL_24546.4 IL_3U5H_054 U 1173 A 1326
UGCCGGAA*UA