Alignment of IL_49751.4 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
3
I

6
4

3
7
4
I

8
5

4
9
5
I

10
6

5
11
6
I

12
7


13
6
I

14
6

6
15
5
I

16
5

7
17
4
I

18
4

8
19
3
I

20
3

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_49751.4_Instance_1 IL_49751.4,IL_8VMA_004,C51_G75CUCCUACUUG
IL_49751.4_Sequence_1 IL_49751.48VMA_C51_G75CUCCU*ACUUGtrue93000.84
IL_49751.4_Instance_2 IL_49751.4,IL_8VMB_003,C51_G72CUCCUACUUG
IL_49751.4_Sequence_2 IL_49751.48VMB_C51_G72CUCCU*ACUUGtrue93000.84
IL_49751.4_Instance_3 IL_49751.4,IL_8VM9_004,C68_G52CUUUGCUCUG
IL_49751.4_Sequence_3 IL_49751.48VM9_C68_G52CUUUG*CUCUGtrue99000.06
IL_49751.4_Instance_4 IL_49751.4,IL_8VM8_003,C54_G78CUCUGCUUUG
IL_49751.4_Sequence_4 IL_49751.48VM8_C54_G78CUCUG*CUUUGtrue100000.00
IL_49751.4_Instance_5 IL_49751.4,IL_8DP3_002,C54_G75CUCUGCUUUG
IL_49751.4_Sequence_5 IL_49751.48DP3_C54_G75CUCUG*CUUUGtrue100000.00
IL_49751.4_Instance_6 IL_49751.4,IL_8SP9_002,C99_G86CUUUGCUCUG
IL_49751.4_Sequence_6 IL_49751.48SP9_C99_G86CUUUG*CUCUGtrue99000.06
IL_49751.4_Instance_7 IL_49751.4,IL_8S95_002,C101_G88CCUUGCUCCG
IL_49751.4_Sequence_7 IL_49751.48S95_C101_G88CCUUG*CUCCGtrue87001.52
IL_49751.4_Instance_8 IL_49751.4,IL_5BTM_001,U10_A46UUCUAUUCUA
IL_49751.4_Sequence_8 IL_49751.45BTM_U10_A46UUCUA*UUCUAtrue85001.67
IL_49751.4_Instance_9 IL_49751.4,IL_7VYX_008,G51_U15GUGCCGACUU
IL_49751.4_Sequence_9 IL_49751.47VYX_G51_U15GUGCC*GACUUtrue69003.48
IL_49751.4_Instance_10 IL_49751.4,IL_7VYX_004,U37_G25UUAUCGGAUG
IL_49751.4_Sequence_10 IL_49751.47VYX_U37_G25UUAUC*GGAUGtrue70003.38
IL_49751.4_Instance_11 IL_49751.4,IL_8P9A_349,G3284_C3166GCGUGCACAC
IL_49751.4_Sequence_11 IL_49751.48P9A_G_3284_C_3166GCGUG*CACACtrue56005.00
IL_49751.4_Instance_12 IL_49751.4,IL_8D29_010,G4_C31GAUACGCAGC
IL_49751.4_Sequence_12 IL_49751.48D29_G4_C31GAUAC*GCAGCtrue70003.43
IL_49751.4_Instance_13 IL_49751.4,IL_4LFB_065,G713_U677GGAACGGAAU
IL_49751.4_Sequence_13 IL_49751.44LFB_G713_U677GGAAC*GGAAUtrue68003.65
IL_49751.4_Instance_14 IL_49751.4,IL_5J7L_361,G713_U677GGAAUAGAAU
IL_49751.4_Sequence_14 IL_49751.45J7L_G713_U677GGAAU*AGAAUtrue67003.70
IL_49751.4_Instance_15 IL_49751.4,IL_4WF9_123,C1768_G1761CCCAGUAGGG
IL_49751.4_Sequence_15 IL_49751.44WF9_C_1768_G_1761CCCAG*UAGGGtrue38006.96
IL_49751.4_Instance_16 IL_49751.4,IL_5VOE_003,C6_G31CCCCAGCCCCG
IL_49751.4_Sequence_16 IL_49751.45VOE_C6_G31CCCCAG*CCCCGtrue42006.51

Conserved interactions between motif group positions in IL_49751.4:
1 2 s35 
1 10 cWW 
2 3 s35 
2 9 cWW 
2 10 s55 
3 4 s35 
3 8 cWW 
3 9 s55 
4 5 s35 
4 7 cWW 
4 8 s55 
5 6 cWW 
5 7 s55 
6 7 s35 
7 8 s35 
8 9 s35 
9 10 s35
JAR3D SCFG/MRF model for IL_49751.4:
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 [10] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.009512849,0.061367376,0.010330796,0.147234463,0.000000000],[0.032008708,0.010038147,0.222423107,0.012144246,0.000000000],[0.010345834,0.160227436,0.002092205,0.095974051,0.000000000],[0.152065850,0.012058410,0.047913011,0.014263510,0.000000000],[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 C51 - G75 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.014610683,0.162714610,0.083545514,0.020292475,0.000000000],[0.047241285,0.074599531,0.033560937,0.018894692,0.000000000],[0.092952240,0.018703469,0.003629925,0.035579588,0.000000000],[0.019131204,0.019262487,0.036097737,0.319183623,0.000000000],[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 [9] // Basepair U52 - U74 cWW 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.146434771,0.016954389,0.031649303,0.052270096,0.000000000],[0.017984699,0.069091423,0.069283919,0.194092548,0.000000000],[0.029673292,0.072428879,0.003474326,0.019047320,0.000000000],[0.061050069,0.182493126,0.020621478,0.013450360,0.000000000],[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 [8] // Basepair C53 - U73 cWW 
BasepairNode | Deletion Probability [0.0000174430812709] | Pair Probability [[0.028768218,0.147641336,0.074773842,0.032663252,0.000000000],[0.052197334,0.123294957,0.031224773,0.016890105,0.000000000],[0.055639805,0.031114718,0.003514026,0.047253650,0.000000000],[0.040788934,0.017444713,0.056761682,0.240028656,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.934446650,0.065203005,0.000340613,0.000009732] | Left Letter Distribution [0.500000000,0.166666667,0.166666667,0.166666667,0.000000000] | Right Length Distribution [0.997990020,0.001999980,0.000010000] | Right Letter Distribution [0.250000000,0.250000000,0.250000000,0.250000000,0.000000000] | Left Index [4] | Right Index [7] // Basepair C54 - C72 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008711103,0.031976113,0.009639697,0.178001370,0.000000000],[0.016385995,0.008657340,0.203674770,0.011323817,0.000000000],[0.009604678,0.230514201,0.001890642,0.048630221,0.000000000],[0.193071306,0.011406145,0.025753097,0.010759505,0.000000000],[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 U55 - A71 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_49751.4:
> IL_49751.4  8VMA C   51 G   75
CUCCU*ACUUG
> IL_49751.4  8VMB C   51 G   72
CUCCU*ACUUG
> IL_49751.4  8VM9 C   68 G   52
CUUUG*CUCUG
> IL_49751.4  8VM8 C   54 G   78
CUCUG*CUUUG
> IL_49751.4  8DP3 C   54 G   75
CUCUG*CUUUG
> IL_49751.4  8SP9 C   99 G   86
CUUUG*CUCUG
> IL_49751.4  8S95 C  101 G   88
CCUUG*CUCCG
> IL_49751.4  5BTM U   10 A   46
UUCUA*UUCUA
> IL_49751.4  7VYX G   51 U   15
GUGCC*GACUU
> IL_49751.4  7VYX U   37 G   25
UUAUC*GGAUG
> IL_49751.4  8P9A G 3284 C 3166
GCGUG*CACAC
> IL_49751.4  8D29 G    4 C   31
GAUAC*GCAGC
> IL_49751.4  4LFB G  713 U  677
GGAAC*GGAAU
> IL_49751.4  5J7L G  713 U  677
GGAAU*AGAAU
> IL_49751.4  4WF9 C 1768 G 1761
CCCAG*UAGGG
> IL_49751.4  5VOE C    6 G   31
CCCCAG*CCCCG