Alignment of IL_13959.4 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


11
5
I

12
5

5
13
4
I

14
4

6
15
3
I

16
3

7
17
2
I

18
2

8
19
1
I


In
acceptance
region


Cutoff
score

Full
edit
distance

Interior
edit
distance

Alignment
score
deficit
IL_13959.4_Instance_1 IL_13959.4_IL_1SAQ_002_C111_G106CGAGCGAG
IL_13959.4_Sequence_1 IL_13959.4_IL_1SAQ_002_C111_G106CGAG*CGAGtrue100000.00
IL_13959.4_Instance_2 IL_13959.4_IL_1SA9_001_C111_G106CGAGCGAG
IL_13959.4_Sequence_2 IL_13959.4_IL_1SA9_001_C111_G106CGAG*CGAGtrue100000.00
IL_13959.4_Instance_3 IL_13959.4_IL_3V2F_086_C2364_G2353CGAGCGAG
IL_13959.4_Sequence_3 IL_13959.4_IL_3V2F_086_C_2364_G_2353CGAG*CGAGtrue100000.00
IL_13959.4_Instance_4 IL_13959.4_IL_2QBG_088_C2364_G2353CGAGCGAG
IL_13959.4_Sequence_4 IL_13959.4_IL_2QBG_088_C_2364_G_2353CGAG*CGAGtrue100000.00
IL_13959.4_Instance_5 IL_13959.4_IL_4IOA_083_C2343_G2332CGAGCGAG
IL_13959.4_Sequence_5 IL_13959.4_IL_4IOA_083_C_2343_G_2332CGAG*CGAGtrue100000.00
IL_13959.4_Instance_6 IL_13959.4_IL_3D0U_002_C67_G19CGAGCGAG
IL_13959.4_Sequence_6 IL_13959.4_IL_3D0U_002_C67_G19CGAG*CGAGtrue100000.00
IL_13959.4_Instance_7 IL_13959.4_IL_4BPP_087_U1682_A1643UAAAUGAA
IL_13959.4_Sequence_7 IL_13959.4_IL_4BPP_087_U_1682_A_1643UAAA*UGAAtrue86001.29
IL_13959.4_Instance_8 IL_13959.4_IL_4BPP_085_U1625_A1700UAACGGAA
IL_13959.4_Sequence_8 IL_13959.4_IL_4BPP_085_U_1625_A_1700UAAC*GGAAtrue88001.15
IL_13959.4_Instance_9 IL_13959.4_IL_3U5F_088_C1729_G1672CAAAUGAG
IL_13959.4_Sequence_9 IL_13959.4_IL_3U5F_088_C_1729_G_1672CAAA*UGAGtrue92000.72
IL_13959.4_Instance_10 IL_13959.4_IL_4A1B_007_C162_G257CAACGGAG
IL_13959.4_Sequence_10 IL_13959.4_IL_4A1B_007_C162_G257CAAC*GGAGtrue94000.58
IL_13959.4_Instance_11 IL_13959.4_IL_2QBG_017_G536_C557GGAGUGAC
IL_13959.4_Sequence_11 IL_13959.4_IL_2QBG_017_G536_C557GGAG*UGACtrue75002.42
IL_13959.4_Instance_12 IL_13959.4_IL_4BPP_003_U37_A462UAAAUGACA
IL_13959.4_Sequence_12 IL_13959.4_IL_4BPP_003_U37_A462UAAA*UGACAtrue58003.96
IL_13959.4_Instance_13 IL_13959.4_IL_4A1B_117_C2993_G3133CGACGGAAAG
IL_13959.4_Sequence_13 IL_13959.4_IL_4A1B_117_C_2993_G_3133CGAC*GGAAAGtrue51004.63
IL_13959.4_Instance_14 IL_13959.4_IL_3U5H_120_C3004_G3144CAAUAGAACG
IL_13959.4_Sequence_14 IL_13959.4_IL_3U5H_120_C_3004_G_3144CAAU*AGAACGtrue39005.75
IL_13959.4_Instance_15 IL_13959.4_IL_1FJG_059_U1481_G1419UGACGGAG
IL_13959.4_Sequence_15 IL_13959.4_IL_1FJG_059_U_1481_G_1419UGAC*GGAGtrue85001.44
IL_13959.4_Instance_16 IL_13959.4_IL_3U5F_013_C186_G199CGACGAAG
IL_13959.4_Sequence_16 IL_13959.4_IL_3U5F_013_C186_G199CGAC*GAAGtrue90000.93
IL_13959.4_Instance_17 IL_13959.4_IL_4IOA_058_U1530_G1494UCAGCAAG
IL_13959.4_Sequence_17 IL_13959.4_IL_4IOA_058_U_1530_G_1494UCAG*CAAGtrue68003.05
IL_13959.4_Instance_18 IL_13959.4_IL_4A1B_005_C138_G128CAACGAAG
IL_13959.4_Sequence_18 IL_13959.4_IL_4A1B_005_C138_G128CAAC*GAAGtrue85001.44
IL_13959.4_Instance_19 IL_13959.4_IL_3U5F_085_C1653_G1747CGAUAGAG
IL_13959.4_Sequence_19 IL_13959.4_IL_3U5F_085_C_1653_G_1747CGAU*AGAGtrue98000.17
IL_13959.4_Instance_20 IL_13959.4_IL_1S72_098_C2873_G2884CGAGCGAG
IL_13959.4_Sequence_20 IL_13959.4_IL_1S72_098_C_2873_G_2884CGAG*CGAGtrue100000.00
IL_13959.4_Instance_21 IL_13959.4_IL_4A1B_132_C3316_G3303CGAUAGAG
IL_13959.4_Sequence_21 IL_13959.4_IL_4A1B_132_C_3316_G_3303CGAU*AGAGtrue98000.17
IL_13959.4_Instance_22 IL_13959.4_IL_3DIR_002_C70_G22CGAGCGAG
IL_13959.4_Sequence_22 IL_13959.4_IL_3DIR_002_C70_G22CGAG*CGAGtrue100000.00
IL_13959.4_Instance_23 IL_13959.4_IL_2AW7_065_U1481_G1419UGACGGAG
IL_13959.4_Sequence_23 IL_13959.4_IL_2AW7_065_U_1481_G_1419UGAC*GGAGtrue85001.44
IL_13959.4_Instance_24 IL_13959.4_IL_3U5H_141_C3360_G3345CGAUAGAG
IL_13959.4_Sequence_24 IL_13959.4_IL_3U5H_141_C_3360_G_3345CGAU*AGAGtrue98000.17
IL_13959.4_Instance_25 IL_13959.4_IL_2IL9_002_A6058_U6021AAUAUAUU
IL_13959.4_Sequence_25 IL_13959.4_IL_2IL9_002_A_6058_U_6021AAUA*UAUUtrue38005.86
IL_13959.4_Instance_26 IL_13959.4_IL_2O3V_002_C7_G42CGCUAAAAG
IL_13959.4_Sequence_26 IL_13959.4_IL_2O3V_002_C7_G42CGCU*AAAAGtrue64003.43

Conserved interactions between motif group positions in IL_13959.4:
1 2 s35 
1 8 cWW 
2 6 s33 
2 7 tSH 
2 8 s55 
3 4 s35 
3 6 tHS 
3 7 s55 
4 5 cWW 
4 6 s55 
5 6 s35 
7 8 s35 
7 2 6BR
3 6 6BR
JAR3D SCFG/MRF model for IL_13959.4:
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 [8] // Initial node C111 - G106 from junction 
BasepairNode | Deletion Probability [0.0000132678587784] | Pair Probability [[0.008294599,0.014312172,0.009576747,0.151456887,0.000000000],[0.044699620,0.007743685,0.298156428,0.011138058,0.000000000],[0.009689343,0.159107771,0.001869446,0.018710913,0.000000000],[0.169069254,0.010625603,0.076296475,0.009253001,0.000000000],[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 [0.921154598,0.040223480,0.038540736,0.000077495,0.000003690] | Right Letter Distribution [0.500000000,0.300000000,0.100000000,0.100000000,0.000000000] | Left Index [1] | Right Index [8] // Basepair C111 - G106 cWW 
BasepairNode | Deletion Probability [0.0000132736577717] | Pair Probability [[0.145487941,0.108926192,0.001227015,0.027212787,0.000000000],[0.105368082,0.081170457,0.001227015,0.001227015,0.000000000],[0.242216542,0.001227015,0.018730957,0.066681200,0.000000000],[0.100258643,0.096585107,0.001227015,0.001227015,0.000000000],[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 [0.882858682,0.116823982,0.000306266,0.000011070] | Right Letter Distribution [0.700000000,0.100000000,0.100000000,0.100000000,0.000000000] | Left Index [2] | Right Index [7] // Basepair G112 - A105 tSH 
BasepairNode | Deletion Probability [0.0000244705618206] | Pair Probability [[0.118163166,0.094541409,0.277534671,0.099817256,0.000000000],[0.115282494,0.088817694,0.001102839,0.096148385,0.000000000],[0.001102839,0.001102839,0.005980668,0.001102839,0.000000000],[0.017117566,0.001102839,0.079979660,0.001102839,0.000000000],[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 [6] // Basepair A113 - G104 tHS 
BasepairNode | Deletion Probability [0.0000249735224443] | Pair Probability [[0.008128108,0.025408901,0.009083861,0.188309537,0.000000000],[0.016113918,0.007225292,0.216116288,0.010127624,0.000000000],[0.009064412,0.232552318,0.001781266,0.038742155,0.000000000],[0.196220574,0.010218194,0.020421330,0.010486221,0.000000000],[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 [4] | Right Index [5] // Basepair G114 - C103 cWW 
HairpinNode  | Num Bases [1] | Left Index [5] | Right Index [5] | 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_13959.4:
> IL_13959.4 IL_1SAQ_002 C  111 G  106
CGAG*CGAG
> IL_13959.4 IL_1SA9_001 C  111 G  106
CGAG*CGAG
> IL_13959.4 IL_3V2F_086 C 2364 G 2353
CGAG*CGAG
> IL_13959.4 IL_2QBG_088 C 2364 G 2353
CGAG*CGAG
> IL_13959.4 IL_4IOA_083 C 2343 G 2332
CGAG*CGAG
> IL_13959.4 IL_3D0U_002 C   67 G   19
CGAG*CGAG
> IL_13959.4 IL_4BPP_087 U 1682 A 1643
UAAA*UGAA
> IL_13959.4 IL_4BPP_085 U 1625 A 1700
UAAC*GGAA
> IL_13959.4 IL_3U5F_088 C 1729 G 1672
CAAA*UGAG
> IL_13959.4 IL_4A1B_007 C  162 G  257
CAAC*GGAG
> IL_13959.4 IL_2QBG_017 G  536 C  557
GGAG*UGAC
> IL_13959.4 IL_4BPP_003 U   37 A  462
UAAA*UGACA
> IL_13959.4 IL_4A1B_117 C 2993 G 3133
CGAC*GGAAAG
> IL_13959.4 IL_3U5H_120 C 3004 G 3144
CAAU*AGAACG
> IL_13959.4 IL_1FJG_059 U 1481 G 1419
UGAC*GGAG
> IL_13959.4 IL_3U5F_013 C  186 G  199
CGAC*GAAG
> IL_13959.4 IL_4IOA_058 U 1530 G 1494
UCAG*CAAG
> IL_13959.4 IL_4A1B_005 C  138 G  128
CAAC*GAAG
> IL_13959.4 IL_3U5F_085 C 1653 G 1747
CGAU*AGAG
> IL_13959.4 IL_1S72_098 C 2873 G 2884
CGAG*CGAG
> IL_13959.4 IL_4A1B_132 C 3316 G 3303
CGAU*AGAG
> IL_13959.4 IL_3DIR_002 C   70 G   22
CGAG*CGAG
> IL_13959.4 IL_2AW7_065 U 1481 G 1419
UGAC*GGAG
> IL_13959.4 IL_3U5H_141 C 3360 G 3345
CGAU*AGAG
> IL_13959.4 IL_2IL9_002 A 6058 U 6021
AAUA*UAUU
> IL_13959.4 IL_2O3V_002 C    7 G   42
CGCU*AAAAG