Alignment of IL_57744.1 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


9
4
I

10
4

4
11
3
I

12
3

5
13
2
I

14
2

6
15
1
I


In
acceptance
region

Cutoff
score
Full
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distance
Interior
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distance
Alignment
score
deficit
IL_57744.1_Instance_1 IL_57744.1,IL_5T3K_001,G7_C28GAAGCAC
IL_57744.1_Sequence_1 IL_57744.15T3K_G7_C28GAAG*CACtrue93000.67
IL_57744.1_Instance_2 IL_57744.1,IL_3TD0_005,G16_C32GAAGCGC
IL_57744.1_Sequence_2 IL_57744.13TD0_G16_C32GAAG*CGCtrue100000.00
IL_57744.1_Instance_3 IL_57744.1,IL_3TD0_002,G39_C9GAAGCGC
IL_57744.1_Sequence_3 IL_57744.13TD0_G39_C9GAAG*CGCtrue100000.00
IL_57744.1_Instance_4 IL_57744.1,IL_8P9A_418,G957_C870GUUUGAC
IL_57744.1_Sequence_4 IL_57744.18P9A_G957_C870GUUU*GACtrue56004.21
IL_57744.1_Instance_5 IL_57744.1,IL_6WBR_001,G26_C43GGAUAC
IL_57744.1_Sequence_5 IL_57744.16WBR_G26_C43GGA*UACtrue86001.34
IL_57744.1_Instance_6 IL_57744.1,IL_7QR8_008,U14_A6UAUAAA
IL_57744.1_Sequence_6 IL_57744.17QR8_U14_A6UAU*AAAtrue77002.20
IL_57744.1_Instance_7 IL_57744.1,IL_4RUM_001,G13_C90GAGCGAC
IL_57744.1_Sequence_7 IL_57744.14RUM_G13_C90GAGC*GACtrue83001.59
IL_57744.1_Instance_8 IL_57744.1,IL_1U6B_001,G19_C31GCCGCAC
IL_57744.1_Sequence_8 IL_57744.11U6B_G19_C31GCCG*CACtrue62003.64
IL_57744.1_Instance_9 IL_57744.1,IL_5UNE_004,C27_G18CAGUAG
IL_57744.1_Sequence_9 IL_57744.15UNE_C27_G18CAG*UAGtrue70002.89
IL_57744.1_Instance_10 IL_57744.1,IL_2QEK_001,G7_C17GAAGCAC
IL_57744.1_Sequence_10 IL_57744.12QEK_G7_C17GAAG*CACtrue93000.67
IL_57744.1_Instance_11 IL_57744.1,IL_7LYF_004,C51_G72CGACGAG
IL_57744.1_Sequence_11 IL_57744.17LYF_C51_G72CGAC*GAGtrue91000.85
IL_57744.1_Instance_12 IL_57744.1,IL_6TFF_003,C34_G25CAGCGGG
IL_57744.1_Sequence_12 IL_57744.16TFF_C34_G25CAGC*GGGtrue88001.16
IL_57744.1_Instance_13 IL_57744.1,IL_4K31_002,A16_U9AAAGCGU
IL_57744.1_Sequence_13 IL_57744.14K31_A16_U9AAAG*CGUtrue96000.41
IL_57744.1_Instance_14 IL_57744.1,IL_5J7L_009,G128_C233GAAAUGC
IL_57744.1_Sequence_14 IL_57744.15J7L_G128_C233GAAA*UGCtrue96000.37
IL_57744.1_Instance_15 IL_57744.1,IL_4K31_003,A16_U9AAAGCGU
IL_57744.1_Sequence_15 IL_57744.14K31_A16_U9AAAG*CGUtrue96000.41
IL_57744.1_Instance_16 IL_57744.1,IL_7D7V_003,C41_G24CAGUGGG
IL_57744.1_Sequence_16 IL_57744.17D7V_C41_G24CAGU*GGGtrue76002.24
IL_57744.1_Instance_17 IL_57744.1,IL_9DFE_040,G1031_C1123GAUGCGC
IL_57744.1_Sequence_17 IL_57744.19DFE_G_1031_C_1123GAUG*CGCtrue95000.44
IL_57744.1_Instance_18 IL_57744.1,IL_5J7L_282,G1031_C1123GAUGCGC
IL_57744.1_Sequence_18 IL_57744.15J7L_G_1031_C_1123GAUG*CGCtrue95000.44
IL_57744.1_Instance_19 IL_57744.1,IL_4WF9_041,G1075_C1167GAUGCGC
IL_57744.1_Sequence_19 IL_57744.14WF9_G_1075_C_1167GAUG*CGCtrue95000.44
IL_57744.1_Instance_20 IL_57744.1,IL_7A0S_038,G1042_C1134GAUGCGC
IL_57744.1_Sequence_20 IL_57744.17A0S_G_1042_C_1134GAUG*CGCtrue95000.44
IL_57744.1_Instance_21 IL_57744.1,IL_5ZTM_001,C162_G120CCGUAG
IL_57744.1_Sequence_21 IL_57744.15ZTM_C162_G120CCG*UAGtrue57004.13
IL_57744.1_Instance_22 IL_57744.1,IL_7D7W_003,C34_G25CAGCGGG
IL_57744.1_Sequence_22 IL_57744.17D7W_C34_G25CAGC*GGGtrue88001.16

Conserved interactions between motif group positions in IL_57744.1:
1 2 s35 
1 6 cWW 
2 5 cWW 
2 6 s55 
3 4 cWW 
3 5 s55 
4 5 s35 
5 6 s35
JAR3D SCFG/MRF model for IL_57744.1:
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 [6] // Initial node
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.008032221,0.016254158,0.009105995,0.184155982,0.000000000],[0.015239427,0.008031998,0.219377157,0.010914397,0.000000000],[0.009072523,0.278419306,0.001741514,0.023494187,0.000000000],[0.174966950,0.011073712,0.021469355,0.008651118,0.000000000],[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 [6] // Basepair G7 - C28 cWW 
BasepairNode | Deletion Probability [0.0000003223953951] | Pair Probability [[0.166399001,0.014257371,0.324672144,0.016633196,0.000000000],[0.048083333,0.009491110,0.017694617,0.031196661,0.000000000],[0.234602578,0.017648448,0.003371478,0.015304541,0.000000000],[0.029271882,0.032748883,0.027203319,0.011421437,0.000000000],[0.000000000,0.000000000,0.000000000,0.000000000,0.000000000]] | Left Length Distribution [0.182901112,0.815134090,0.001872216,0.000092582] | Left Letter Distribution [0.425000000,0.075000000,0.225000000,0.275000000,0.000000000] | 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 [5] // Basepair A8 - A27 cWW 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008626261,0.037041618,0.009603658,0.163007117,0.000000000],[0.036436504,0.009664800,0.177657300,0.011170114,0.000000000],[0.009570628,0.236692128,0.001921763,0.061844213,0.000000000],[0.153887491,0.011327515,0.060267879,0.011281012,0.000000000],[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 [3] | Right Index [4] // Basepair G10 - C26 cWW 
HairpinNode  | Num Bases [1] | Left Index [4] | Right Index [4] | 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_57744.1:
> IL_57744.1  5T3K G    7 C   28
GAAG*CAC
> IL_57744.1  3TD0 G   16 C   32
GAAG*CGC
> IL_57744.1  3TD0 G   39 C    9
GAAG*CGC
> IL_57744.1  8P9A G  957 C  870
GUUU*GAC
> IL_57744.1  6WBR G   26 C   43
GGA*UAC
> IL_57744.1  7QR8 U   14 A    6
UAU*AAA
> IL_57744.1  4RUM G   13 C   90
GAGC*GAC
> IL_57744.1  1U6B G   19 C   31
GCCG*CAC
> IL_57744.1  5UNE C   27 G   18
CAG*UAG
> IL_57744.1  2QEK G    7 C   17
GAAG*CAC
> IL_57744.1  7LYF C   51 G   72
CGAC*GAG
> IL_57744.1  6TFF C   34 G   25
CAGC*GGG
> IL_57744.1  4K31 A   16 U    9
AAAG*CGU
> IL_57744.1  5J7L G  128 C  233
GAAA*UGC
> IL_57744.1  4K31 A   16 U    9
AAAG*CGU
> IL_57744.1  7D7V C   41 G   24
CAGU*GGG
> IL_57744.1  9DFE G 1031 C 1123
GAUG*CGC
> IL_57744.1  5J7L G 1031 C 1123
GAUG*CGC
> IL_57744.1  4WF9 G 1075 C 1167
GAUG*CGC
> IL_57744.1  7A0S G 1042 C 1134
GAUG*CGC
> IL_57744.1  5ZTM C  162 G  120
CCG*UAG
> IL_57744.1  7D7W C   34 G   25
CAGC*GGG