Alignment of IL_85647.3 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

3
7
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
6

6
13
7
I

14
8

7
15
8
I

16
9

8
17
9
I

18
10


19
9
I

20
9

9
21
8
I

22
8

10
23
7
I

24
6

11
25
5
I

26
5

12
27
4
I

28
4

13
29
3
I

30
3

14
31
2
I

32
2

15
33
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_85647.3_Instance_1 IL_85647.3_IL_1Q96_001_C6_G24CUCAGUAUAGAACCG
IL_85647.3_Sequence_1 IL_85647.3_IL_1Q96_001_C6_G24CUCAGUAU*AGAACCGtrue91001.75
IL_85647.3_Instance_2 IL_85647.3_IL_1JBR_001_C6_G24CUCAGUACGGAACCG
IL_85647.3_Sequence_2 IL_85647.3_IL_1JBR_001_C6_G24CUCAGUAC*GGAACCGtrue92001.58
IL_85647.3_Instance_3 IL_85647.3_IL_1Q96_003_C6_G24CUCAGUAUAGAACCG
IL_85647.3_Sequence_3 IL_85647.3_IL_1Q96_003_C6_G24CUCAGUAU*AGAACCGtrue91001.75
IL_85647.3_Instance_4 IL_85647.3_IL_3U5H_122_C3018_G3036CUUAGUACGGAACAG
IL_85647.3_Sequence_4 IL_85647.3_IL_3U5H_122_C_3018_G_3036CUUAGUAC*GGAACAGtrue89002.15
IL_85647.3_Instance_5 IL_85647.3_IL_4A1B_003_C80_G101CCCAGUAAUGAACAG
IL_85647.3_Sequence_5 IL_85647.3_IL_4A1B_003_C80_G101CCCAGUAA*UGAACAGtrue87002.61
IL_85647.3_Instance_6 IL_85647.3_IL_4IOA_007_G215_C236GUUAGUAGCGAACCC
IL_85647.3_Sequence_6 IL_85647.3_IL_4IOA_007_G215_C236GUUAGUAG*CGAACCCtrue89002.23
IL_85647.3_Instance_7 IL_85647.3_IL_3V2F_006_C201_G194CUCAGUACGGAACUG
IL_85647.3_Sequence_7 IL_85647.3_IL_3V2F_006_C201_G194CUCAGUAC*GGAACUGtrue100000.00
IL_85647.3_Instance_8 IL_85647.3_IL_2QBG_011_C201_G194CUAAGUACGGAACUG
IL_85647.3_Sequence_8 IL_85647.3_IL_2QBG_011_C201_G194CUAAGUAC*GGAACUGtrue98000.35
IL_85647.3_Instance_9 IL_85647.3_IL_4A1B_118_G3007_C3025GUUAGUACGGAACAC
IL_85647.3_Sequence_9 IL_85647.3_IL_4A1B_118_G_3007_C_3025GUUAGUAC*GGAACACtrue88002.38
IL_85647.3_Instance_10 IL_85647.3_IL_1S72_006_C171_G164CUCAGUAUAGAACUG
IL_85647.3_Sequence_10 IL_85647.3_IL_1S72_006_C171_G164CUCAGUAU*AGAACUGtrue99000.17
IL_85647.3_Instance_11 IL_85647.3_IL_4IOA_006_C178_G171CUCAGUACGGAACUG
IL_85647.3_Sequence_11 IL_85647.3_IL_4IOA_006_C178_G171CUCAGUAC*GGAACUGtrue100000.00
IL_85647.3_Instance_12 IL_85647.3_IL_4A1C_008_G71_C104GUUAGUACGGAAGUC
IL_85647.3_Sequence_12 IL_85647.3_IL_4A1C_008_G71_C104GUUAGUAC*GGAAGUCtrue87002.69
IL_85647.3_Instance_13 IL_85647.3_IL_3V2F_046_A1262_U2017AUGAGUAAUGAAAUU
IL_85647.3_Sequence_13 IL_85647.3_IL_3V2F_046_A_1262_U_2017AUGAGUAA*UGAAAUUtrue97000.56
IL_85647.3_Instance_14 IL_85647.3_IL_3U5H_148_A72_U106ACCGAGUAGCGAAACU
IL_85647.3_Sequence_14 IL_85647.3_IL_3U5H_148_A72_U106ACCGAGUAG*CGAAACUtrue73005.56
IL_85647.3_Instance_15 IL_85647.3_IL_2QBG_048_A1262_U2017AUAAGUAAUGAAAUU
IL_85647.3_Sequence_15 IL_85647.3_IL_2QBG_048_A_1262_U_2017AUAAGUAA*UGAAAUUtrue95001.01
IL_85647.3_Instance_16 IL_85647.3_IL_4IOA_047_A1275_U2000AUGAGUAAUGAAAUU
IL_85647.3_Sequence_16 IL_85647.3_IL_4IOA_047_A_1275_U_2000AUGAGUAA*UGAAAUUtrue97000.56

Conserved interactions between motif group positions in IL_85647.3:
1 2 s35 
1 15 cWW 
2 3 s35 
2 14 cWW 
2 15 s55 
3 4 s33 
3 13 tSH 
4 5 s55 
4 6 s55 
4 11 s53 
4 12 tHH 
5 6 cSH 
5 10 s33 
6 7 s35 
6 10 s33 
6 11 tWH 
7 8 s35 
7 10 tHS 
7 11 s55 
8 9 cWW 
8 10 s55 
9 10 s35 
11 12 s35 
12 13 s35 
13 14 s35 
14 15 s35 
10 6 6BPh
5 11 6BPh
4 12 6BPh
13 3 6BR
7 10 6BR
JAR3D SCFG/MRF model for IL_85647.3:
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 [15] // Initial node C6 - G24 from junction 
BasepairNode | Deletion Probability [0.0000174430812709] | Pair Probability [[0.008675828,0.017305933,0.009868939,0.208763802,0.000000000],[0.017525751,0.007668670,0.260538742,0.011333681,0.000000000],[0.009914276,0.206893488,0.001889988,0.022419314,0.000000000],[0.172878144,0.011132189,0.022745860,0.010445394,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.934446650,0.065203005,0.000340613,0.000009732] | Left Letter Distribution [0.166666667,0.500000000,0.166666667,0.166666667,0.000000000] | 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 [15] // Basepair C6 - G24 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.012043709,0.122205117,0.011969405,0.029253075,0.000000000],[0.035781168,0.089520195,0.019193391,0.013829750,0.000000000],[0.011822882,0.019450683,0.004113380,0.037329396,0.000000000],[0.061924409,0.088229224,0.017064970,0.426269247,0.000000000],[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 [14] // Basepair U7 - C23 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.094201538,0.129338943,0.001354713,0.006427133,0.000000000],[0.106675245,0.182885554,0.001354713,0.001354713,0.000000000],[0.147691304,0.001354713,0.006637998,0.038275031,0.000000000],[0.118683445,0.146725775,0.015684468,0.001354713,0.000000000],[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 [3] | Right Index [13] // Basepair C8 - C22 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.617640543,0.095681848,0.023662502,0.023698462,0.000000000],[0.008744982,0.000677143,0.058212869,0.048098828,0.000000000],[0.004230257,0.056186787,0.001658919,0.000677143,0.000000000],[0.004161052,0.055314377,0.000677143,0.000677143,0.000000000],[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 [4] | Right Index [12] // Basepair A9 - A21 tHH 
ClusterNode  | Deletion Probability [0.0000001250000000] | Num Left Bases [2] | Num Right Bases [1] | Left Index [5] | Right Index [11] | Norm Constant [0.511983607588030] // Cluster node G10:U11 and A20:A20
Interaction  | Interacting Bases [2,3] | Pair Probability [[0.022837272,0.004789512,0.023493607,0.004789512,0.000000000],[0.047574079,0.039764490,0.031792035,0.004789512,0.000000000],[0.004789512,0.004789512,0.056052332,0.022341674,0.000000000],[0.616882239,0.004789512,0.059086009,0.051439190,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction U11 - A20 tWH 
Interaction  | Interacting Bases [1,2] | Pair Probability [[0.048479644,0.049942729,0.002723713,0.002253535,0.000000000],[0.046894616,0.054472179,0.000579310,0.054897273,0.000000000],[0.033155631,0.018131255,0.037062536,0.543447746,0.000000000],[0.004171512,0.048578946,0.000579310,0.054630067,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] // Cluster Interaction G10 - U11 cSH 
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 [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [7] | Right Index [10] // New Initial node after Cluster
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.038440127,0.038782129,0.462139192,0.041783058,0.000000000],[0.044806889,0.040649327,0.003242082,0.040252647,0.000000000],[0.000463155,0.000463155,0.015707204,0.000463155,0.000000000],[0.002205483,0.000463155,0.269676090,0.000463155,0.000000000],[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 [7] | Right Index [10] // Basepair A12 - G19 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008515984,0.017593209,0.009557680,0.211161401,0.000000000],[0.018336446,0.007836719,0.240176240,0.010785029,0.000000000],[0.009597611,0.195328240,0.001890644,0.022188538,0.000000000],[0.202408459,0.010607771,0.023000835,0.011015193,0.000000000],[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 [8] | Right Index [9] // Basepair U13 - A18 cWW 
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_85647.3:
> IL_85647.3 IL_1Q96_001 C    6 G   24
CUCAGUAU*AGAACCG
> IL_85647.3 IL_1JBR_001 C    6 G   24
CUCAGUAC*GGAACCG
> IL_85647.3 IL_1Q96_003 C    6 G   24
CUCAGUAU*AGAACCG
> IL_85647.3 IL_3U5H_122 C 3018 G 3036
CUUAGUAC*GGAACAG
> IL_85647.3 IL_4A1B_003 C   80 G  101
CCCAGUAA*UGAACAG
> IL_85647.3 IL_4IOA_007 G  215 C  236
GUUAGUAG*CGAACCC
> IL_85647.3 IL_3V2F_006 C  201 G  194
CUCAGUAC*GGAACUG
> IL_85647.3 IL_2QBG_011 C  201 G  194
CUAAGUAC*GGAACUG
> IL_85647.3 IL_4A1B_118 G 3007 C 3025
GUUAGUAC*GGAACAC
> IL_85647.3 IL_1S72_006 C  171 G  164
CUCAGUAU*AGAACUG
> IL_85647.3 IL_4IOA_006 C  178 G  171
CUCAGUAC*GGAACUG
> IL_85647.3 IL_4A1C_008 G   71 C  104
GUUAGUAC*GGAAGUC
> IL_85647.3 IL_3V2F_046 A 1262 U 2017
AUGAGUAA*UGAAAUU
> IL_85647.3 IL_3U5H_148 A   72 U  106
ACCGAGUAG*CGAAACU
> IL_85647.3 IL_2QBG_048 A 1262 U 2017
AUAAGUAA*UGAAAUU
> IL_85647.3 IL_4IOA_047 A 1275 U 2000
AUGAGUAA*UGAAAUU